Plant Pathogen Populations Research Articles

New insights into mycotoxin risk management through fungal population genetics and genomics.

Mycotoxin contamination of food and feed is a major global concern. Chronic or acute dietary exposure to contaminated food and feed can negatively affect both human and animal health. Contamination occurs through plant infection by toxigenic fungi, primarily Aspergillus and Fusarium spp., either before or after harvest. Despite the application of various management strategies, controlling these pathogens remains a major challenge primarily because of their ability to adapt to environmental changes and selection pressures. Understanding the genetic structure of plant pathogen populations is pivotal for gaining new insights into their biology and epidemiology, as well as for understanding the mechanisms behind their adaptability. Such deeper understanding is crucial for developing effective and preemptive management strategies tailored to the evolving nature of pathogenic populations. This review focuses on the population-level variations within the two most economically significant toxigenic fungal genera according to space, host, and pathogenicity. Outcomes in terms of migration patterns, gene flow within populations, mating abilities, and the potential for host jumps are examined. We also discuss effective yet often underutilized applications of population genetics and genomics to address practical challenges in the epidemiology and disease control of toxigenic fungi.

The effect of quantitative wheat resistance on the aggressiveness of Fusarium graminearum.

Little is known about the selection pressures acting on plant pathogen populations, especially those applied by quantitative forms of resistance. Fusarium graminearum causes Fusarium Head Blight (FHB) in wheat, producing significant yield losses and mycotoxin contamination. Quantitative host resistance is the best method to control FHB. However, there needs to be more understanding of how disease resistance affects the evolution of plant pathogens. This study aimed to determine if the presence or absence of wheat resistance influenced the fitness components and genomic regions of F. graminearum. Thirty-one isolates from highly susceptible and 25 isolates from moderately resistant wheat lines were used. Isolate aggressiveness was measured by area under the disease progress curve (AUDPC), visually damaged kernels, and deoxynivalenol contamination. In vitro growth rate and spore production were also measured. Two whole-genome scans for selection were conducted with 333,297 SNPs. One scan looked for signatures of selection in the entire sample and the other scan was for divergent selection between the isolates from moderately resistant wheat and highly susceptible wheat. The population of isolates from highly susceptible wheat was primarily aggressive. Several regions of the F. graminearum genome with signatures for selection were identified. The moderately resistant wheat varieties used in this study did not select more aggressive isolates, suggesting that quantitative resistance is a durable method to control FHB.

Strategies for managing fungicide resistance in the Brazilian tropical agroecosystem: Safeguarding food safety, health, and the environmental quality

AbstractFungicide resistance is an alarming challenge for the Brazilian tropical agricultural systems, with major implications for food safety, human and animal health, as well as for the environment. This review explores strategies to address fungicide resistance within the Brazilian agroecosystem context. We examined historical and current scenarios of fungicide resistance in the Brazilian agroecosystems and the approaches to delay the emergence and mitigate the selection of resistant variants. Our review indicates that the prevalence of resistance in field populations of key plant pathogens in Brazil was due to failures in the implementation of preventive measures. To address this issue, alternative evolutionary-smart strategies against fungicide resistance are proposed, emphasizing institutional actions and public policies. Crucial steps involve strengthening national networks for large-scale foliar and seed fungicide efficacy testing and resistance monitoring, as well as imposing tighter restrictions on the labeling of high-risk single-active formulations. Additionally, the integration of non-chemical disease management strategies and the establishment of a centralized database and information system on fungicide resistance in Brazil are identified as essential for effective resistance monitoring and informed decision-making. To enhance fungicide resistance management, the adoption of a warning system (e.g., based on aerobiology- or on weather-monitoring) for predicting disease epidemics and minimizing fungicide applications is recommended. Increased funding, collaboration, mandatory reporting, and capacity building are required to overcome these challenges. In addition, promoting integrated disease management approaches is vital. By implementing these tailored strategies, Brazil can actively contribute to safeguarding its food safety, protecting human and animal health, and preserving the delicate balance of its unique agroecosystem. The adoption of evolutionary-smart strategies against fungicide resistance will prolong fungicide efficacy, reduce economic costs, and minimize environmental impacts, ensuring sustainable and resilient agriculture in Brazil.

Deep amplicon sequencing reveals extensive allelic diversity in the erg11/CYP51 promoter and allows multi-population DMI fungicide resistance monitoring in the canola pathogen Leptosphaeria maculans

Continued use of fungicides provides a strong selection pressure towards strains with mutations to render these chemicals less effective. Previous research has shown that resistance to the demethylation inhibitor (DMI) fungicides, which target ergosterol synthesis, in the canola pathogen Leptosphaeria maculans has emerged in Australia and Europe. The change in fungicide sensitivity of individual isolates was found to be due to DNA insertions into the promoter of the erg11/CYP51 DMI target gene. Whether or not these were the only types of mutations and how prevalent they were in Australian populations was explored in the current study. New isolates with reduced DMI sensitivity were obtained from screens on DMI-treated plants, revealing eight independent insertions in the erg11 promoter. A novel deep amplicon sequencing approach applied to populations of ascospores fired from stubble identified an additional undetected insertion allele and quantified the frequencies of all known insertions, suggesting that, at least in the samples processed, the combined frequency of resistant alleles is between 0.0376% and 32.6%. Combined insertion allele frequencies positively correlated with population-level measures of in planta resistance to four different DMI treatments. Additionally, there was no evidence for erg11 coding mutations playing a role in conferring resistance in Australian populations. This research provides a key method for assessing fungicide resistance frequency in stubble-borne populations of plant pathogens and a baseline from which additional surveillance can be conducted in L. maculans. Whether or not the observed resistance allele frequencies are associated with loss of effective disease control in the field remains to be established.

Metagenomic Study of Fungal Microbial Communities in Two PDO Somontano Vineyards (Huesca, Spain): Effects of Age, Plant Genotype, and Initial Phytosanitary Status on the Priming and Selection of their Associated Microorganisms.

The study of microbial communities associated with different plants of agronomic interest has allowed, in recent years, to answer a number of questions related to the role and influence of certain microbes in key aspects of their autoecology, such as improving the adaptability of the plant host to different abiotic or biotic stresses. In this study, we present the results of the characterization, through both high-throughput sequencing and classical microbiological methods, of the fungal microbial communities associated with grapevine plants in two vineyards of different ages and plant genotypes located in the same biogeographical unit. The study is configured as an approximation to the empirical demonstration of the concept of "microbial priming" by analyzing the alpha- and beta-diversity present in plants from two plots subjected to the same bioclimatic regime to detect differences in the structure and taxonomic composition of the populations. The results were compared with the inventories of fungal diversity obtained by culture-dependent methods to establish, where appropriate, correlations between both microbial communities. Metagenomic data showed a differential enrichment of the microbial communities in the two vineyards studied, including the populations of plant pathogens. This is tentatively explained due to factors such as the different time of exposure to microbial infection, different plant genotype, and different starting phytosanitary situation. Thus, results suggest that each plant genotype recruits differential fungal communities and presents different profiles of associated potential microbial antagonists or communities of pathogenic species.

Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere?

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays; however, they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.

How large and diverse are field populations of fungal plant pathogens? The case of Zymoseptoria tritici.

Pathogen populations differ in the amount of genetic diversity they contain. Populations carrying higher genetic diversity are thought to have a greater evolutionary potential than populations carrying less diversity. We used published studies to estimate the range of values associated with two critical components of genetic diversity, the number of unique pathogen genotypes and the number of spores produced during an epidemic, for the septoria tritici blotch pathogen Zymoseptoria tritici. We found that wheat fields experiencing typical levels of infection are likely to carry between 3.1 and 14.0 million pathogen genotypes per hectare and produce at least 2.1–9.9 trillion pycnidiospores per hectare. Given the experimentally derived mutation rate of 3 × 10−10 substitutions per site per cell division, we estimate that between 27 and 126 million pathogen spores carrying adaptive mutations to counteract fungicides and resistant cultivars will be produced per hectare during a growing season. This suggests that most of the adaptive mutations that have been observed in Z. tritici populations can emerge through local selection from standing genetic variation that already exists within each field. The consequences of these findings for disease management strategies are discussed.

Fungal plant pathogens observed on perennial cereal crops in New York during 2017–2018

AbstractPerennial grain crops are emerging as a promising addition to sustainable agricultural systems because of their low-input requirements and delivery of ecosystem services. However, adoption of these crops is expected to bring novel management challenges, including those related to plant diseases. In New York, fungal pathogens of annual grains have a significant impact on crop yield and value and are generally controlled through a combination of host resistances, cultural practices and chemical fungicides. Without the availability of crop rotation and soil tillage practices, disease control in perennial grain systems may be problematic, and little is known about perennial grain crop susceptibility to local plant pathogen populations. During 2017 and 2018, ongoing field trials of two perennial grain crops recently introduced in New York, intermediate wheatgrass (IWG; Thinopyrum intermedium) and perennial cereal rye (PCR; Secale cereale), were assessed for the presence of putative fungal pathogens on actively growing plants, overwintered crop residue and harvested grain. A total of nine potential host–pathogen combinations were recorded based on symptomology, pathogen morphology and DNA sequences. Common annual crop pathogens were recovered most frequently, but, at one site, Phyllachora graminis, causal fungus of tar spot and a pathogen not previously reported on crops in New York, was found on IWG. Residue colonization by an important toxigenic pathogen (Fusarium graminearum) was high in both crops, though mycotoxin levels in associated grain were low, indicating either the hosts or environment were unsuitable for disease development. Seed-borne fungal communities differed across crops and locations, and black point, a condition caused by Alternaria and Bipolaris fungi and indicative of compromised grain quality, was prevalent in PCR under some conditions. Growing PCR with intercropped red clover (Trifolium pratense L.) resulted in less Stagonospora colonization of stem residue, and PCR grown with an oat (Avena sativa L.) nurse crop had a reduced incidence of black point. These alternative cultural practices may prove useful for managing disease in perennial grains. Our results suggest that the incorporation of perennial crops into the agricultural landscape will lead to familiar plant disease problems requiring new solutions as well as new problems that may require significant research investments.

Integration of Stalk Destruction Methods for the Glyphosate Herbicide-Resistant Cotton

The increase in geographical areas used for cultivation of transgenic glyphosate herbicide-resistant cotton has hindered the stalk destruction, compromised the phytosanitary break implementation and consequently increased the population of insect pests and cotton plant pathogens. This study evaluated the efficiency of the combining mechanical and chemical methods in the destruction of transgenic cotton stalk resistant to the glyphosate herbicide. Two experiments were carried out in 2015 and 2016 in Primavera do Leste, Mato Grosso, Brazil and Luís Eduardo Magalhães, Bahia, Brazil, respectively. The study evaluated different mechanical destruction equipment in combination with the chemical methods. In each environment, a randomized block experiment with four replications was employed. The results of the experiments indicated that the mechanical destruction increased the control efficiency by at least 10% when compared to chemical destruction of the cotton stalk. Chemical destruction with herbicides combined with mechanical destruction methods does not increase the control efficiency of cotton stalks destruction. Furthermore, the application of hormonal herbicides following the mechanical shredding of cotton stalks does not increase the control efficiency of glyphosate-resistant cotton stalk.

Genetic Analysis of Plant Pathogens Natural Populations.

Population genetics allow to address fundamental questions about the biology of plant pathogens. By testing specific hypotheses, population genetics provide insights into the population genetic variability of pathogens across different geographical areas, time, and associated plant hosts, as well as on the structure and differentiation of populations, and on the possibility that a population is introduced and from where it has originated. In this chapter, basic concepts of population genetics are introduced, as well as the five evolutionary factors affecting populations, that is, mutations, recombination, variation in population size, gene flow, and natural selection. A step-by-step workflow, from sampling to data analysis, on how to perform a genetic analysis of natural populations of plant pathogens is discussed. Increased knowledge of the population biology of pathogens is pivotal to improve management strategies of diseases in agricultural and forest ecosystems.

Biologická ochrana patogenních hub: budou hrát mykoviry důležitou úlohu?

In the past few years, huge economic and environmental losses have resulted by fungal pathogens in agriculture and food production worldwide. Fungal toxins also pose a threat for food production and animal health. In the last decade, the site-specific fungicides has been used in plant protection, providing highly efficient protection against phytopathogens. However, the use of pesticides boosted problems with resistance in the targeted organisms and increased negative environmental impact of insecticides, herbicides and fungicides. Therefore, new methods are needed to control resistant populations of plant pathogens, including fungi. Mycoviruses are fungal viruses, i.e. viruses infecting fungi. Some mycoviruses affect the growth and virulence of the host fungus and may prevent successful infection of plant host. They have potential to reduce phytopathogens. In this review, the successful examples how mycoviruses alter hypovirulence in well-known phytopathogens are discussed. Mycoviruses could be useful as a one of new next generation pest-control products.

Patterns of thermal adaptation in a globally distributed plant pathogen: Local diversity and plasticity reveal two-tier dynamics.

Plant pathogen populations inhabit patchy environments with contrasting, variable thermal conditions. We investigated the diversity of thermal responses in populations sampled over contrasting spatiotemporal scales, to improve our understanding of their dynamics of adaptation to local conditions. Samples of natural populations of the wheat pathogen Zymoseptoria tritici were collected from sites within the Euro‐Mediterranean region subject to a broad range of climatic conditions. We tested for local adaptation, by accounting for the diversity of responses at the individual and population levels on the basis of key thermal performance curve parameters and “thermotype” (groups of individuals with similar thermal responses) composition. The characterization of phenotypic responses and genotypic structure revealed the following: (i) a high degree of individual plasticity and variation in sensitivity to temperature conditions across spatiotemporal scales and populations; and (ii) geographic variation in thermal response among populations, with major alterations due to seasonal patterns over the wheat‐growing season. The seasonal shifts in functional composition suggest that populations are locally structured by selection, contributing to adaptation patterns. Further studies combining selection experiments and modeling are required to determine how functional group selection drives population dynamics and adaptive potential in response to thermal heterogeneity.

Using structural variants to understand the ecological and evolutionary dynamics of fungal plant pathogens.

Deletions, duplications, insertions, inversions and translocations are commonly referred to as structural variants (SVs). Fungal plant pathogens have compact genomes, facilitating the generation of accurate maps of SVs for these species in recent studies. Structural variants have been found to constitute a significant proportion of the standing genetic variation in fungal plant pathogen populations, potentially leading to the generation of accessory genes, regions or chromosomes enriched in pathogenicity factors. Structural variants are involved in the rapid adaptation and ecological traits of pathogens, including host specialization and mating. Long-read sequencing techniques coupled with theoretical and experimental approaches have considerable potential for elucidating the phenotypic effects of SVs and deciphering the evolutionary and genomic mechanisms underlying the formation of SVs in fungal plant pathogens.

Allopatric Plant Pathogen Population Divergence following Disease Emergence.

Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce's disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia.IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce's disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.

Suppression Effects on Pineapple Soil-Borne Pathogens by Crotalaria juncea, Dolomitic Lime and Plastic Mulch Cover on MD-2 Hybrid Cultivar

The development and implementation of sustainable and environmentally friendly agricultural practices are indispensable as alternatives to pesticide use and to keep populations of soil-borne plant pathogens at levels that do not affect crop productivity. The present research evaluates the incidence of soil-borne phytopathogens on the pineapple variety MD-2, which was subjected to different treatments: Incorporation of <i>Crotalaria juncea</i> into the soil (organic amendment), application of dolomitic lime to soil (inorganic amendment), and the use of plastic mulch covering the soil. During the crop cycle (15 months), the following variables were evaluated: plant height (cm), fruit weight (kg·plant⁻¹ ), crop yield (ton·ha⁻¹ ), the bud root disease incidence caused by <i>Phytophthora nicotianae</i>, number of soil phytoparasitic nematodes and colony-forming-units (CFUs) of soil fungi and oomycetes. The results indicate that <i>Crotalaria juncea</i> treatment reduced the pathogen population (nematode and oomycetes) at levels that did not affect crop development, so that yield increased (18–20%). The incorporation of <i>C. juncea</i> into the soil as an organic amendment favors the populations of fungi disease suppressors (<i>Trichoderma-Aspergillus</i>). The phytoparasitic nematodes (<i>Meloidogyne</i> sp., <i>Pratylenchus</i> sp., and <i>Mesocriconema</i> sp.) and oomycetes (<i>Phytophthora</i> spp., and <i>Pythium</i> spp.) showed a reduction of their population levels by effects of organic amendment (<i>C. juncea</i>). The plastic mulch was also effective, probably due to the maintenance of optimal condition to crop growth and weed control. However, the dolomitic lime application had the poorest effect under the conditions of the study area on the variables analyzed. The described observations are characteristics of a system-based approach for the potential management of soil-borne pathogens of pineapple MD-2 in Veracruz, México.

NOD-like receptor-mediated plant immunity: from structure to cell death.

Animal and plant immune systems use intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) to detect pathogens, resulting in the activation of immune responses that are often associated with localized host cell death. Whereas vertebrate NLRs detect evolutionarily conserved molecular patterns and have undergone comparatively little copy number expansion, plant NLRs detect virulence factors that have often diversified in plant pathogen populations, and thus plant NLRs have been subject to parallel diversification. Plant NLRs sense the presence of virulence factors with enzymatic virulence activity often indirectly through their modification of host target proteins. By contrast, phytopathogenic virulence factors without enzymatic activity are usually recognized by NLRs directly by their structure. Structural and biochemical analyses have shown that both indirect and direct recognition of plant pathogens trigger the oligomerization of plant NLRs into active complexes. Assembly into three-layered ring-like structures has emerged as a common principle of NLR activation in plants and animals, but with distinct amino-terminal domains initiating different signalling pathways. Collectively, these analyses point to host cell membranes as a convergence point for activated plant NLRs and the disruption of cellular ion homeostasis as a possible major factor in NLR-triggered cell death signalling.

Deciphering the modes of action of Golubevia sp., an antagonist against the causal agent of powdery mildew in wheat, using an mRNA-based systems approach

Biocontrol agents are living organisms with the potential to suppress populations of plant pathogens or pests in a cropping system. The complex interplay between the different players and the changing environment, results in a combination of different modes of action. Here, we applied an mRNA-based systems approach to gain insight into the antagonist-pathogen-host interaction of Golubevia sp. isolates BC0812 and BC0850 with the causal agent of wheat powdery mildew, Blumeria graminis f. sp. tritici, in planta over time. Bioassays were performed on potted wheat plants (water-treated control, antagonist, pathogen, antagonist+pathogen) under controlled conditions. A significantly higher percentage of mildew conidia were parasitized after treatment with Golubevia sp. BC0812 with 26% and BC0850 with 16% compared to the water control with 1%. Differential gene expression analysis of antagonists, pathogen and host 5, 6, 7, and 11 days after inoculation (dai) with the antagonist pointed to a combination of different modes of action: An interplay of modulating plant defense responses, impairing conidiogenesis of the pathogen by scavenging H2O2, facultative hyperparasitism and nitrogen competition. Microscopic observations supported the suggested hyperparasitism as thin mycelium could be observed on Bgt conidia at 6 dai and later.Taken together the results allowed the formulation of new hypothesis regarding modes of action and the interplay between antagonist, pathogen and host. It showed that a solid molecular understanding of the antagonist-pathogen relationship over time is essential for less biased mode of action studies. Understanding this complex interplay is the basis for targeted optimization strategies and allows discovery of new potential targets and markers for future biocontrol development.

Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields.

The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region.IMPORTANCE Rhizosphere fungi play key roles in ecosystems as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management may influence rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but it also maintains a greater richness of saprotrophic, plant-pathogenic, and mycoparasitic fungi that has implications for the efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.

Involvement of Jasmonic Acid in the Induced Systemic Resistance of Tomato against Ralstonia syzigiisub sp. indonesiensis by Indigenous Endophyte Bacteria

Endophyte bacteria colonize plant roots and exert a beneficial effect on plant growth are well known for their potential to reduce plant pathogen populations in the soil, thereby suppressing diseases. Elucidation of signaling pathways controlling disease resistance is a major objective in research on plant-pathogen interactions. It has been suggested that jasmonic acid (JA) could be an integral part of a general signal transduction system regulating inducible defense genes in plants. Recent studies had shown that Endophyte bacteria could elicited induce systemic resistance (ISR) of plants by jasmonic acid pathway. This research purposed to study the involvement of JA in ISR of tomato plants against Ralstonia syzigiisubsp. Indonesiensis by indigenous endophyte bacteria. This research assayed the JA contained in the leaves and roots of tomato plants that treated with indigenous endophyte bacteria (seed and seedlings treatment) and inoculated with R. syzigiisub sp. Indonesiensis with Gas Chromatography-Mass Spectrophotometry (GC-MS) in interval between 0 to 30 days after pathogen innoculation. Results shown that all selected indigenous endophyte bacteria can suppress R. syzigiisub sp. Indonesiensis attack and increase JA contained in leaves and roots of tomato significantly until 12 days after pathogen innoculations. Strain Bacillus cereus EPL1.1.3 and Serratianematodiphila TLE1.1 respectively had the highest JA activivity both in roots and leaves of tomato. This indicated that one of the selected indigenous endophyte bacteria abilities to suppress pathogens attack mechanism related to JA pathway.

The yeast (Saccharomyces cerevisiae) YCF1 vacuole transporter: Evidence on its implication into the yeast resistance to flusilazole as revealed by GC/EI/MS metabolomics

The development of plant protection product (PPPs)-resistant populations of plant pathogens, pests, and weeds, represents a major challenge that the crop protection sector is facing. Focusing on plant pathogenic fungi, the increased efflux of the active ingredients (a.i.) from the cytoplasm is highly correlated to elevated resistance levels to the applied fungicides. Such mechanism is regulated by ATP-binding cassette transporters (ABC transporters), and although it has been investigated for the past two decades, the latest developments in “omics” technologies could provide new insights with potential applications in crop protection. Within this context, and based on results from preliminary experiments, we have undertaken the task of mining the involvement of the ABC transporter YCF1, which is located in the vacuole membrane, in the fungicide resistance development, applying a functional genomics approach and using yeast (Saccharomyces cerevisiae) as the model organism. Among the fungicides being assessed, flusilazole, which belongs to the azole group of dimethylation inhibitors (DMIs), was discovered as a possible substrate of the YCF1. GC/EI/MS metabolomics analysis revealed the effect of the fungicide's toxicity and that of genotype on yeast's metabolism, confirming the role of this transporter. Fluctuations in the activity of various yeast biosynthetic pathways associated with stress responses were recorded, and corresponding metabolites-biomarkers of flusilazole toxicity were discovered. The metabolites α,α-trehalose, glycerol, myo-inositol-1-phosphate, GABA, l-glutamine, l-tryptophan, l-phenylalanine, l-tyrosine, and phosphate, were the major identified biomarkers of toxicity. Among these, are metabolites that play important roles in fungal metabolism (e.g., cell responses to osmotic stress) or serve as signaling molecules. To the best of our knowledge, this is the first report on the implication of YCF1 in fungal resistance to PPPs. Additionally, the results of GC/EI/MS yeast metabolomics confirmed the robustness of the method and its applicability in the high-throughput study of fungal resistance to fungicides.