Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum

Profiling Metabolites with Antifungal Activities from Endophytic Plant-Beneficial Strains of Pseudomonas chlororaphis Isolated from Chamaecytisus albus (Hack.) Rothm

Fungal phytopathogens represent a large and economically significant challenge to food production worldwide. Thus, the application of biocontrol agents can be an alternative. In the present study, we carried out biological, metabolomic, and genetic analyses of three endophytic isolates from nodules of Chamaecytisus albus, classified as Pseudomonas chlororaphis acting as antifungal agents. The efficiency of production of their diffusible and volatile antifungal compounds (VOCs) was verified in antagonistic assays with the use of soil-borne phytopathogens: B. cinerea, F. oxysporum, and S. sclerotiorum. Diffusible metabolites were identified using chromatographic and spectrometric analyses (HPTLC, GC-MS, and LC-MS/MS). The phzF, phzO, and prnC genes in the genomes of bacterial strains were confirmed by PCR. In turn, the plant growth promotion (PGP) properties (production of HCN, auxins, siderophores, and hydrolytic enzymes, phosphate solubilization) of pseudomonads were bioassayed. The data analysis showed that all tested strains have broad-range antifungal activity with varying degrees of antagonism. The most abundant bioactive compounds were phenazine derivatives: phenazine-1-carboxylic acid (PCA), 2-hydroxy-phenazine, and diketopiperazine derivatives as well as ortho-dialkyl-aromatic acids, pyrrolnitrin, siderophores, and HCN. The results indicate that the tested P. chlororaphis isolates exhibit characteristics of biocontrol organisms; therefore, they have potential to be used in sustainable agriculture and as commercial postharvest fungicides to be used in fruits and vegetables.

High-Resolution Disease Phenotyping Reveals Distinct Resistance Mechanisms of Tomato Crop Wild Relatives against Sclerotinia sclerotiorum

Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a bottleneck in deciphering QDR's genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag-phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost (<1.000 €) phenotyping system to measure lesion growth dynamics of wild tomato species (e.g., Solanum pennellii or Solanum pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR mechanisms and their cross-talk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance mechanisms. The results of our study show how QDR can be maintained by facilitating different defense mechanisms during host-parasite interaction and that the capacity of the QDR toolbox highly depends on the host's genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.

Exploitation of microbial activities at low pH to enhance planetary health

Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is, however, under-recognized that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization, processing, and preservation of food. For circular economy, microbial metabolism would be exploited to produce building blocks for the chemical industry, to achieve effective crop protection, agri-food waste revalorization, or biofuel production, as well as in bioremediation and bioaugmentation of contaminated areas. Low pH is undoubtedly a key physical-chemical parameter that needs to be considered for exploiting the powerful microbial metabolic arsenal. Deviation from optimal pH conditions has profound effects on shaping the microbial communities responsible for carrying out essential processes. Furthermore, novel strategies to combat contaminations and infections by pathogens rely on microbial-derived acidic molecules that suppress/inhibit their growth. Herein, we present the state-of-the-art of the knowledge on the impact of acidic pH in many applied areas and how this knowledge can guide us to use the immense arsenal of microbial metabolic activities for their more impactful exploitation in a Planetary Health perspective.

Impact of Sclerotinia sclerotiorum Infection on Lettuce (Lactuca sativa L.) Survival and Phenolics Content-A Case Study in a Horticulture Farm in Poland

Sclerotinia sclerotiorum is a cause of a prevalent and destructive disease that attacks many horticultural food crops, such as lettuce. This soil-borne necrotrophic fungal pathogen causes significant economic losses in worldwide lettuce production annually. Furthermore, current methods utilized for management and combatting the disease, such as biocontrol, are insufficient. In this study, three cultivars of lettuce (one Crispy and two Leafy cultivars of red and green lettuce) were grown in central Poland (Lodz Voivodeship), a widely known Polish horticultural region. In the summer and early autumn, lettuce cultivars were grown in control and S. sclerotiorum-infected fields. The lettuce cultivars (Templin, Lollo Rossa, and Lollo Bionda) differed phenotypically and in terms of the survival of the fungal infection. The Crispy iceberg Templin was the most susceptible to S. sclerotiorum infection compared to the other cultivars during both vegetation seasons. The total content of phenolic compounds, flavonoids, and anthocyanins varied among cultivars and fluctuated during infection. Moreover, phenolic content was affected by vegetation season with alterable environmental factors such as air temperature, humidity, soil temperature, and pH. The most increased levels of phenolics, both flavonoids and anthocyanins in infected plants, were observed in the Leafy red Lollo Rossa cultivar in both crops. However, the highest survival/resistance to the fungus was noticed for Lollo Rossa in the summer crop and Lollo Bionda in the autumn crop.

Antifungal activity of cyclopaldic acid from Antarctic Penicillium against phytopathogenic fungi

Plant pathogens cause great economic losses in agriculture. To reduce damage, chemical pesticides have been frequently used, but these compounds in addition to causing risks to the environment and health, its continuous use has given rise to resistant phytopathogens, threatening the efficiency of control methods. One alternative for such a problem is the use of natural products with high antifungal activity and low toxicity. Here, we present the production, isolation, and identification of cyclopaldic acid, a bioactive compound produced by Penicillium sp. CRM 1540, a fungal strain isolated from Antarctic marine sediment. The crude extract was fractionated by reversed-phase chromatography and yielded 40 fractions, from which fraction F17 was selected. We used 1D and 2D Nuclear Magnetic Resonance analysis in DMSO-d6 and CDCl3, together with mass spectrometry, to identify the compound as cyclopaldic acid C11H10O6 (238 Da). The pure compound was evaluated for antimicrobial activity against phytopathogenic fungi of global agricultural importance, namely: Macrophomina phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. The antifungal assay revealed the potential of cyclopaldic acid, produced by Penicillium sp. CRM 1540, as a leading molecule against M. phaseolina and R. solani, with more than 90% of growth inhibition after 96h of contact with the fungal cells using 100 µg mL-1, and more than 70% using 50 µg mL-1.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03792-9.

Overview and Management of the Most Common Eukaryotic Diseases of Flax (Linum usitatissimum)

Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.

Exploring the molecular basis of resistance to Botrytis cinerea in chickpea genotypes through biochemical and morphological markers

Chickpea (Cicer arietinum L.) is an important pulse crop around the globe and a valuable source of protein in the human diet. However, it is highly susceptible to various plant pathogens such as fungi, bacteria, and viruses, which can cause significant damage from the seedling phase until harvest, leading to reduced yields and affecting its production. Botrytis cinerea can cause significant damage to chickpea crops, especially under high humidity and moisture conditions. This fungus can cause grey mould disease, which can lead to wilting, stem and pod rot, and reduced yields. Chickpea plants have developed specific barriers to counteract the harmful effects of this fungus. These barriers include biochemical and structural defences. In this study, the defence responses against B. cinerea were measured by the quantification of biochemical metabolites such as antioxidant enzymes, malondialdehyde (MDA), proline, glutathione (GSH), H₂O₂, ascorbic acid (AA) and total phenol in the leaf samples of chickpea genotypes (one accession of wild Cicer species, viz. Cicer pinnatifidum188 identified with high level of resistance to Botrytis grey mould (BGM) and a cultivar, Cicer arietinumPBG5 susceptible to BGM grown in the greenhouse). Seedlings of both the genotypes were inoculated with (1 × 10⁴ spore mL^-1) inoculum of isolate 24, race 510 of B. cinerea and samples were collected after 1, 3, 5, and 7 days post-inoculation (dpi). The enhanced enzymatic activity was observed in the pathogen-inoculated leaf samples as compared to uninoculated (healthy control). Among inoculated genotypes, the resistant one exhibited a significant change in enzymatic activity, total phenolic content, MDA, proline, GSH, H₂O₂, and AA, compared to the susceptible genotype. The study also examined the isozyme pattern of antioxidant enzymes at various stages of B. cinerea inoculation. Results from scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy revealed that BGM had a more significant impact on susceptible genotypes compared to resistant ones when compared to the control (un-inoculated). In addition, SEM and FTIR spectroscopy analyses confirmed the greater severity of BGM on susceptible genotypes compared to their resistant counterparts. Our results suggest the role of antioxidant enzymes and other metabolites as defence tools and biochemical markers to understand compatible and non-compatible plant-pathogen interactions better. The present investigation will assist future plant breeding programs aimed at developing resistant varieties.

Botrytis cinerea tolerates phytoalexins produced by Solanaceae and Fabaceae plants through an efflux transporter BcatrB and metabolizing enzymes

Botrytis cinerea, a plant pathogenic fungus with a wide host range, has reduced sensitivity to fungicides as well as phytoalexins, threatening cultivation of economically important fruits and vegetable crops worldwide. B. cinerea tolerates a wide array of phytoalexins, through efflux and/or enzymatic detoxification. Previously, we provided evidence that a distinctive set of genes were induced in B. cinerea when treated with different phytoalexins such as rishitin (produced by tomato and potato), capsidiol (tobacco and bell pepper) and resveratrol (grape and blueberry). In this study, we focused on the functional analyses of B. cinerea genes implicated in rishitin tolerance. LC/MS profiling revealed that B. cinerea can metabolize/detoxify rishitin into at least 4 oxidized forms. Heterologous expression of Bcin08g04910 and Bcin16g01490, two B. cinerea oxidoreductases upregulated by rishitin, in a plant symbiotic fungus Epichloë festucae revealed that these rishitin-induced enzymes are involved in the oxidation of rishitin. Expression of BcatrB, encoding an exporter of structurally unrelated phytoalexins and fungicides, was significantly upregulated by rishitin but not by capsidiol and was thus expected to be involved in the rishitin tolerance. Conidia of BcatrB KO (ΔbcatrB) showed enhanced sensitivity to rishitin, but not to capsidiol, despite their structural similarity. ΔbcatrB showed reduced virulence on tomato, but maintained full virulence on bell pepper, indicating that B. cinerea activates BcatrB by recognizing appropriate phytoalexins to utilize it in tolerance. Surveying 26 plant species across 13 families revealed that the BcatrB promoter is mainly activated during the infection of B. cinerea in plants belonging to the Solanaceae, Fabaceae and Brassicaceae. The BcatrB promoter was also activated by in vitro treatments of phytoalexins produced by members of these plant families, namely rishitin (Solanaceae), medicarpin and glyceollin (Fabaceae), as well as camalexin and brassinin (Brassicaceae). Consistently, ΔbcatrB showed reduced virulence on red clover, which produces medicarpin. These results suggest that B. cinerea distinguishes phytoalexins and induces differential expression of appropriate genes during the infection. Likewise, BcatrB plays a critical role in the strategy employed by B. cinerea to bypass the plant innate immune responses in a wide variety of important crops belonging to the Solanaceae, Brassicaceae and Fabaceae.

Control of white mold (Sclerotinia sclerotiorum) through plant-mediated RNA interference

The causative agent of white mold, Sclerotinia sclerotiorum, is capable of infecting over 600 plant species and is responsible for significant crop losses across the globe. Control is currently dependent on broad-spectrum chemical agents that can negatively impact the agroecological environment, presenting a need to develop alternative control measures. In this study, we developed transgenic Arabidopsis thaliana (AT1703) expressing hairpin (hp)RNA to silence S. sclerotiorum ABHYDROLASE-3 and slow infection through host induced gene silencing (HIGS). Leaf infection assays show reduced S. sclerotiorum lesion size, fungal load, and ABHYDROLASE-3 transcript abundance in AT1703 compared to wild-type Col-0. To better understand how HIGS influences host-pathogen interactions, we performed global RNA sequencing on AT1703 and wild-type Col-0 directly at the site of S. sclerotiorum infection. RNA sequencing data reveals enrichment of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway, as well as transcription factors predicted to regulate plant immunity. Using RT-qPCR, we identified predicted interacting partners of ABHYDROLASE-3 in the polyamine synthesis pathway of S. sclerotiorum that demonstrate co-reduction with ABHYDROLASE-3 transcript levels during infection. Together, these results demonstrate the utility of HIGS technology in slowing S. sclerotiorum infection and provide insight into the role of ABHYDROLASE-3 in the A. thaliana-S. sclerotiorum pathosystem.

Fruit-Based Fermented Beverages: Contamination Sources and Emerging Technologies Applied to Assure Their Safety

The food and beverage market has become broader due to globalization and consumer claims. Under the umbrella of consumer demands, legislation, nutritional status, and sustainability, the importance of food and beverage safety must be decisive. A significant sector of food production is related to ensuring fruit and vegetable conservation and utilization through fermentation. In this respect, in this review, we critically analyzed the scientific literature regarding the presence of chemical, microbiological and physical hazards in fruit-based fermented beverages. Furthermore, the potential formation of toxic compounds during processing is also discussed. In managing the risks, biological, physical, and chemical techniques can reduce or eliminate any contaminant from fruit-based fermented beverages. Some of these techniques belong to the technological flow of obtaining the beverages (i.e., mycotoxins bound by microorganisms used in fermentation) or are explicitly applied for a specific risk reduction (i.e., mycotoxin oxidation by ozone). Providing manufacturers with information on potential hazards that could jeopardize the safety of fermented fruit-based drinks and strategies to lower or eliminate these hazards is of paramount importance.

The Botrytis cinerea Gene Expression Browser

For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.

Early warning and diagnostic visualization of Sclerotinia infected tomato based on hyperspectral imaging

This research explored the feasibility of early warning and diagnostic visualization of Sclerotinia infected tomato by using hyperspectral imaging technology. Healthy tomato plants and tomato plants with Sclerotinia sclerotiorum were cultivated, and hyperspectral images at 400-1000 nm were collected from healthy and infected tomato leaves at 1, 3, 5, and 7 days of incubation. After preprocessing the spectra with first derivative (FD), second derivative (SD), standard normal variant (SNV), and multiplicative scatter correction (MSC) partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM) were used to construct tomato sclerotinia identification model and select the best preprocessing method. On this basis, two band screening methods, competitive adaptive reweighted sampling (CARS) and successive projections algorithm (SPA), were introduced to reduce data redundancy and improve the model's prediction accuracy. The results showed that the accuracy of the validation sets and operation speed of the CARS-PLS and CARS-SVM models were 87.88% and 1.8 s, and 87.95% and 1.78 s, respectively. The experiment was based on the SNV-CARS-SVM prediction model combined with image processing, spectral extraction, and visualization analysis methods to create diagnostic visualization software, which opens a new avenue to the implementation of online monitoring and early warning system for sclerotinia infected tomato.

Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants

The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.

Virulence-related metabolism is activated in Botrytis cinerea mostly in the interaction with tolerant green grapes that remain largely unaffected in contrast with susceptible green grapes

Botrytis cinerea is responsible for the gray mold disease, severely affecting Vitis vinifera grapevine and hundreds of other economically important crops. However, many mechanisms of this fruit-pathogen interaction remain unknown. The combined analysis of the transcriptome and metabolome of green fruits infected with B. cinerea from susceptible and tolerant genotypes was never performed in any fleshy fruit, mostly because green fruits are widely accepted to be resistant to this fungus. In this work, peppercorn-sized fruits were infected in the field or mock-treated, and berries were collected at green (EL32) stage from a susceptible (Trincadeira) and a tolerant (Syrah) variety. RNAseq and GC-MS data suggested that Syrah exhibited a pre-activated/basal defense relying on specific signaling pathways, hormonal regulation, namely jasmonate and ethylene metabolisms, and linked to phenylpropanoid metabolism. In addition, putative defensive metabolites such as shikimic, ursolic/ oleanolic, and trans-4-hydroxy cinnamic acids, and epigallocatechin were more abundant in Syrah than Trincadeira before infection. On the other hand, Trincadeira underwent relevant metabolic reprogramming upon infection but was unable to contain disease progression. RNA-seq analysis of the fungus in planta revealed an opposite scenario with higher gene expression activity within B. cinerea during infection of the tolerant cultivar and less activity in infected Trincadeira berries. The results suggested an activated virulence state during interaction with the tolerant cultivar without visible disease symptoms. Together, this study brings novel insights related to early infection strategies of B. cinerea and the green berry defense against necrotrophic fungi.

Transcriptome Profiling Reveals Molecular Players in Early Soybean-Sclerotinia sclerotiorum Interaction

Sclerotinia sclerotiorum causes Sclerotinia stem rot on soybean. Using RNA sequencing, the transcriptomes of the soybean host and the S. sclerotiorum pathogen were simultaneously determined at 4 and 8 h postinoculation (hpi). Two soybean genotypes were involved: a resistant oxalate oxidase (OxO)-transgenic line and its susceptible parent, AC Colibri (AC). Of the 594 genes that were significantly induced by S. sclerotiorum, both hosts expressed genes related to jasmonic acid, ethylene, oxidative burst, and phenylpropanoids. In all, 36% of the differentially expressed genes encoded genes associated with transcription factors, ubiquitination, or general signaling transduction such as receptor-like kinases, mitogen-activated protein kinase kinases, and hormones. No significant differentially expressed genes were identified between genotypes, suggesting that oxalic acid (OA) did not play a differential role in early disease development or primary lesion formation under the conditions used. Looking at pathogen behavior through its gene expression during infection, thousands of genes in S. sclerotiorum were induced at 8 hpi, compared with expression in culture. Many plant cell-wall-degrading enzymes (PCWDEs), sugar transport genes, and genes involved in secondary metabolism were upregulated and could contribute to early pathogenesis. When infecting the OxO plants, there was a higher induction of genes encoding OA, botcinic acid, PCWDEs, proteases, and potential effectors, revealing the wealth of virulence factors available to this pathogen as it attempts to colonize a host. Data presented identify hundreds of genes associated with the very early stages of infection for both the host and pathogen.

SsAGM1-Mediated Uridine Diphosphate-N-Acetylglucosamine Synthesis Is Essential for Development, Stress Response, and Pathogenicity of Sclerotinia sclerotiorum

The necrotrophic fungus Sclerotinia sclerotiorum is a devastating pathogen. S. sclerotiorum can cause Sclerotinia stem rot in more than 600 species of plants, which results in serious economic losses every year. Chitin is one of the most important polysaccharides in fungal cell walls. Chitin and β-Glucan form a scaffold that wraps around the cell and determines the vegetative growth and pathogenicity of pathogens. UDP-GlcNAc is a direct precursor of chitin synthesis. During the synthesis of UDP-GlcNAc, the conversion of GlcNAc-6P to GlcNAc-1P that is catalyzed by AGM1 (N-acetylglucosamine-phosphate mutase) is a key step. However, the significance and role of AGM1 in phytopathogenic fungus are unclear. We identified a cytoplasm-localized SsAGM1 in S. sclerotiorum, which is homologous to AGM1 of Saccharomyces cerevisiae. We utilized RNA interference (RNAi) and overexpression to characterize the function of SsAGM1 in S. sclerotiorum. After reducing the expression of SsAGM1, the contents of chitin and UDP-GlcNAc decreased significantly. Concomitantly, the gene-silenced transformants of SsAGM1 slowed vegetative growth and, importantly, lost the ability to produce sclerotia and infection cushion; it also lost virulence, even on wounded leaves. In addition, SsAGM1 was also involved in the response to osmotic stress and inhibitors of cell wall synthesis. Our results revealed the function of SsAGM1 in the growth, development, stress response, and pathogenicity in S. sclerotiorum.

Double-stranded RNA targeting fungal ergosterol biosynthesis pathway controls Botrytis cinerea and postharvest grey mould

Pathogenic fungi cause major postharvest losses. During storage and ripening, fruit becomes highly susceptible to fungi that cause postharvest disease. Fungicides are effective treatments to limit disease. However, due to increased public concern for their possible side effects, there is a need to develop new strategies to control postharvest fungal pathogens. Botrytis cinerea, a common postharvest pathogen, was shown to uptake small double-stranded RNA (dsRNA) molecules from the host plant. Such dsRNA can regulate gene expression through the RNA interference system. This work aimed to develop a synthetic dsRNA simultaneously targeting three essential transcripts active in the fungal ergosterol biosynthesis pathway (dsRNA-ERG). Our results show initial uptake of dsRNA in the emergence zone of the germination tube that spreads throughout the fungus and results in down-regulation of all three targeted transcripts. Application of dsRNA-ERG decreased B. cinerea germination and growth in in vitro conditions and various fruits, leading to reduce grey-mould decay. The inhibition of growth or decay was reversed by the addition of ergosterol. While dual treatment with dsRNA-ERG and ergosterol-inhibitor fungicide reduced by 100-fold the required amount of fungicide to achieve the same protection rate. The application of dsRNA-ERG induced systemic protection as shown by decreased decay development at inoculation points distant from the treatment point in tomato and pepper fruits. Overall, this study suggests that dsRNA-ERG can effectively control B. cinerea growth and grey-mould development suggesting its efficacy as a future method for postharvest control of fungal pathogens.

Elucidation of the biochemical and molecular basis of the differential disease expression in two cultivars of chili (Capsicum annuum) in response to Colletotrichum capsici infection

Chili plants are affected by the hemibiotrophic ascomycota fungus Colletotrichum capsici causing Anthracnose. Infection results in yield and marketability loss due to a decrease in the quality of fruits. The study of morphological symptom development in two cultivars, Bullet, and Beldanga, showed very different disease expression pattern. To understand the reasons behind such differential response, we investigated, in a time-dependent manner, biochemical activities of important defense enzymes, PR proteins, like peroxidase, polyphenol-oxidase, phenylalanine ammonia lyase, β-glucanase, chitinase, catalase, as well as phenols, flavonoids, chlorophyll and the key signaling molecule nitric oxide in their leaves. We further performed real-time nitric oxide (NO) detection studies. The results showed striking differences in the activity profile of these defense molecules through the course of the study. We monitored the gene expression levels of 12 important defense-related genes under in vivo condition. The transcription levels were mostly increased in the tolerant cultivar till 7 days post-infection (DPI), while downregulation of some of the genes were observed in the susceptible one. These data indicated that disease manifestation is a simulated response of these defense molecules which can nullify the effect of the pathogen and its products, when resistance occurs. Alternatively, the pathogen suppresses the host defense when the disease develops.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11738-021-03334-x.

SsATG8 and SsNBR1 mediated-autophagy is required for fungal development, proteasomal stress response and virulence in Sclerotinia sclerotiorum

Autophagy plays vital roles in the interaction between the necrotrophic fungal pathogen Sclerotinia sclerotiorum and its hosts. However, so far, only little is known about the impacts of autophagy machinery in S. sclerotiorum per se on the fungal morphogenesis and pathogenesis. Here, through functional genomic approaches, we showed that SsATG8, one of the core components of the autophagy machinery, and its interactor SsNBR1, an autophagy cargo receptor, are important for vegetative growth, sclerotial formation, oxalic acid (OA) production, compound appressoria development, and virulence of S. sclerotiorum. Complementation assays with chimeric fusion constructs revealed that both LDS [AIM (ATG8 interacting motif) / LIR (LC3-interacting region) docking site] and UDS [UIM (ubiquitin-interacting motif) docking site] sites of the SsATG8 are required for its functions in autophagy and pathogenesis. Importantly, ΔSsatg8 and ΔSsnbr1 mutants showed enhanced sensitivity to the exogenous treatment with the proteasome inhibitors bortezomib and carfilzomib, and ΔSsnbr1 mutant had decreased expression of SsATG8 under the proteasomal stress conditions, suggesting that a cross-talk exists between ubiquitin-proteasome and selective autophagy pathways, which enables downstream protein degradation to proceed properly during diverse biological processes. Collectively, our data indicate that SsATG8- and SsNBR1-mediated autophagy is crucial for S. sclerotiorum development, proteasomal stress response and virulence.

Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits

The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.

Mechanostimulation: a promising alternative for sustainable agriculture practices

Plants memorize events associated with environmental fluctuations. The integration of environmental signals into molecular memory allows plants to cope with future stressors more efficiently-a phenomenon that is known as 'priming'. Primed plants are more resilient to environmental stresses than non-primed plants, as they are capable of triggering more robust and faster defence responses. Interestingly, exposure to various forms of mechanical stimuli (e.g. touch, wind, or sound vibration) enhances plants' basal defence responses and stress tolerance. Thus, mechanostimulation appears to be a potential priming method and a promising alternative to chemical-based priming for sustainable agriculture. According to the currently available method, mechanical treatment needs to be repeated over a month to alter plant growth and defence responses. Such a long treatment protocol restricts its applicability to fast-growing crops. To optimize the protocol for a broad range of crops, we need to understand the molecular mechanisms behind plant mechanoresponses, which are complex and depend on the frequency, intervals, and duration of the mechanical treatment. In this review, we synthesize the molecular underpinnings of plant mechanoperception and signal transduction to gain a mechanistic understanding of the process of mechanostimulated priming.

Host susceptibility factors render ripe tomato fruit vulnerable to fungal disease despite active immune responses

The increased susceptibility of ripe fruit to fungal pathogens poses a substantial threat to crop production and marketability. Here, we coupled transcriptomic analyses with mutant studies to uncover critical processes associated with defense and susceptibility in tomato (Solanum lycopersicum) fruit. Using unripe and ripe fruit inoculated with three fungal pathogens, we identified common pathogen responses reliant on chitinases, WRKY transcription factors, and reactive oxygen species detoxification. We established that the magnitude and diversity of defense responses do not significantly impact the interaction outcome, as susceptible ripe fruit mounted a strong immune response to pathogen infection. Then, to distinguish features of ripening that may be responsible for susceptibility, we utilized non-ripening tomato mutants that displayed different susceptibility patterns to fungal infection. Based on transcriptional and hormone profiling, susceptible tomato genotypes had losses in the maintenance of cellular redox homeostasis, while jasmonic acid accumulation and signaling coincided with defense activation in resistant fruit. We identified and validated a susceptibility factor, pectate lyase (PL). CRISPR-based knockouts of PL, but not polygalacturonase (PG2a), reduced susceptibility of ripe fruit by >50%. This study suggests that targeting specific genes that promote susceptibility is a viable strategy to improve the resistance of tomato fruit against fungal disease.

Validation of an in vitro system to trigger changes in the gene expression of effectors of Sclerotinia sclerotiorum

AIMS

Sclerotinia sclerotiorum, the causal agent of white mold, can infect several host species, including economically important crops. In this study, we propose and validate a new in vitro system able to mimic the conditions of interaction with the host and promote the induction of S. sclerotiorum effectors.

METHODS AND RESULTS

For culture media production, we selected three plant species, common bean (Phaseolus vulgaris L, cv. Requinte.), maize (Zea mays, cv. BRS1030) and beggarticks (Bidens pilosa). To validate this system as an in vitro inducer of effectors, the qRT-PCR technique was used to investigate the expression profile of some S. sclerotiorum effector genes in each growth medium at different times after inoculation.

CONCLUSION

The results obtained in this study provide a validation of a new method to study S. sclerotiorum during mimetic interaction with different hosts. Although leaf extract does not fully represent the plant environment, the presence of plant components in the culture medium seems to induce effector genes, mimicking in planta conditions. The use of MEVM is simpler than in planta growth, bypasses problems such as the amount of mycelium produced, as well as contamination of host cells during transcriptomic and proteomic analyses.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have devised MEVM media as a model mimicking the interaction of S. sclerotiorum and its hosts and used it to evaluate in vitro expression of effectors normally expressed only in planta.

Genome-wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families

Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant-pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3' receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high-confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection.

Tackling Control of a Cosmopolitan Phytopathogen: Sclerotinia

Phytopathogenic members of the Sclerotinia genus cause widespread disease across a broad range of economically important crops. In particular, Sclerotinia sclerotiorum is considered one of the most destructive and cosmopolitan of plant pathogens. Here, were review the epidemiology of the pathogen, its economic impact on agricultural production, and measures employed toward control of disease. We review the broad approaches required to tackle Sclerotinia diseases and include cultural practices, crop genetic resistance, chemical fungicides, and biological controls. We highlight the benefits and drawbacks of each approach along with recent advances within these controls and future strategies.

Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis

Sclerotinia head rot (SHR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating sunflower crop diseases. Despite its worldwide occurrence, the genetic determinants of plant resistance are still largely unknown. Here, we investigated the Sclerotinia-sunflower pathosystem by analysing temporal changes in gene expression in one susceptible and two tolerant inbred lines (IL) inoculated with the pathogen under field conditions. Differential expression analysis showed little overlapping among ILs, suggesting genotype-specific control of cell defense responses possibly related to differences in disease resistance strategies. Functional enrichment assessments yielded a similar pattern. However, all three ILs altered the expression of genes involved in the cellular redox state and cell wall remodeling, in agreement with current knowledge about the initiation of plant immune responses. Remarkably, the over-representation of long non-coding RNAs (lncRNA) was another common feature among ILs. Our findings highlight the diversity of transcriptional responses to SHR within sunflower breeding lines and provide evidence of lncRNAs playing a significant role at early stages of defense.

Menadione Sodium Bisulfite-Protected Tomato Leaves against Grey Mould via Antifungal Activity and Enhanced Plant Immunity

Tomato grey mould has been one of the destructive fungal diseases during tomato production. Ten mM of menadione sodium bisulfite (MSB) was applied to tomato plants for eco-friendly control of the grey mould. MSB-reduced tomato grey mould in the 3rd true leaves was prolonged at least 7 days prior to the fungal inoculation of two inoculum densities (2 × 10⁴ and 2 × 10⁵ conidia/ml) of Botrytis cinerea. Protection efficacy was significantly higher in the leaves inoculated with the lower disease pressure of conidial suspension compared to the higher one. MSB-pretreatment was not effective to arrest oxalic acid-triggered necrosis on tomato leaves. Plant cell death and hydrogen peroxide accumulation were restricted in necrotic lesions of the B. cinereainoculated leaves by the MSB-pretreatment. Decreased conidia number and germ-tube elongation of B. cinerea were found at 10 h, and mycelial growth was also impeded at 24 h on the MSB-pretreated leaves. MSBmediated disease suppressions were found in cotyledons and different positions (1st to 5th) of true leaves inoculated with the lower conidial suspension, but only 1st to 3rd true leaves showed decreases in lesion sizes by the higher inoculum density. Increasing MSB-pretreatment times more efficiently decreased the lesion size by the higher disease pressure. MSB led to inducible expressions of defence-related genes SlPR1a, SlPR1b, SlPIN2, SlACO1, SlChi3, and SlChi9 in tomato leaves prior to B. cinerea infection. These results suggest that MSB pretreatment can be a promising alternative to chemical fungicides for environment-friendly management of tomato grey mould.

Rapid identification of an Arabidopsis NLR gene as a candidate conferring susceptibility to Sclerotinia sclerotiorum using time-resolved automated phenotyping

The broad host range necrotrophic fungus Sclerotinia sclerotiorum is a devastating pathogen of many oil and vegetable crops. Plant genes conferring complete resistance against S. sclerotiorum have not been reported. Instead, plant populations challenged by S. sclerotiorum exhibit a continuum of partial resistance designated as quantitative disease resistance (QDR). Because of their complex interplay and their small phenotypic effect, the functional characterization of QDR genes remains limited. How broad host range necrotrophic fungi manipulate plant programmed cell death is for instance largely unknown. Here, we designed a time-resolved automated disease phenotyping pipeline enabling high-throughput disease lesion measurement with high resolution, low footprint at low cost. We could accurately recover contrasted disease responses in several pathosystems using this system. We used our phenotyping pipeline to assess the kinetics of disease symptoms caused by seven S. sclerotiorum isolates on six A. thaliana natural accessions with unprecedented resolution. Large effect polymorphisms common to the most resistant A. thaliana accessions identified highly divergent alleles of the nucleotide-binding site leucine-rich repeat gene LAZ5 in the resistant accessions Rubezhnoe and Lip-0. We show that impaired LAZ5 expression in laz5.1 mutant lines and in A. thaliana Rub natural accession correlate with enhanced QDR to S. sclerotiorum. These findings illustrate the value of time-resolved image-based phenotyping for unravelling the genetic bases of complex traits such as QDR. Our results suggest that S. sclerotiorum manipulates plant sphingolipid pathways guarded by LAZ5 to trigger programmed cell death and cause disease.

Phylotranscriptomics of the Pentapetalae Reveals Frequent Regulatory Variation in Plant Local Responses to the Fungal Pathogen Sclerotinia sclerotiorum

Quantitative disease resistance (QDR) is a conserved form of plant immunity that limits infections caused by a broad range of pathogens. QDR has a complex genetic determinism. The extent to which molecular components of the QDR response vary across plant species remains elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold diseases on hundreds of plant species, triggers QDR in host populations. To document the diversity of local responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptomes of six species spanning the Pentapetalae (Phaseolus vulgaris, Ricinus communis, Arabidopsis [Arabidopsis thaliana], Helianthus annuus, Solanum lycopersicum, and Beta vulgaris) inoculated with the same strain of S. sclerotiorum About one-third of plant transcriptomes responded locally to S. sclerotiorum, including a high proportion of broadly conserved genes showing frequent regulatory divergence at the interspecific level. Evolutionary inferences suggested a trend toward the acquisition of gene induction relatively recently in several lineages. Focusing on a group of ABCG transporters, we propose that exaptation by regulatory divergence contributed to the evolution of QDR. This evolutionary scenario has implications for understanding the QDR spectrum and durability. Our work provides resources for functional studies of gene regulation and QDR molecular mechanisms across the Pentapetalae.

Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens

Pathogen infection triggers extensive reprogramming of the plant transcriptome, including numerous genes the function of which is unknown. Due to their wide taxonomic distribution, genes encoding proteins with Domains of Unknown Function (DUFs) activated upon pathogen challenge likely play important roles in disease. In Arabidopsis thaliana, we identified thirteen genes harboring a DUF4228 domain in the top 10% most induced genes after infection by the fungal pathogen Sclerotinia sclerotiorum. Based on functional information collected through homology and contextual searches, we propose to refer to this domain as the pathogen and abiotic stress response, cadmium tolerance, disordered region-containing (PADRE) domain. Genome-wide and phylogenetic analyses indicated that PADRE is specific to plants and diversified into 10 subfamilies early in the evolution of Angiosperms. PADRE typically occurs in small single-domain proteins with a bipartite architecture. PADRE N-terminus harbors conserved sequence motifs, while its C-terminus includes an intrinsically disordered region with multiple phosphorylation sites. A pangenomic survey of PADRE genes expression upon S. sclerotiorum inoculation in Arabidopsis, castor bean, and tomato indicated consistent expression across species within phylogenetic groups. Multi-stress expression profiling and co-expression network analyses associated AtPADRE genes with the induction of anthocyanin biosynthesis and responses to chitin and to hypoxia. Our analyses reveal patterns of sequence and expression diversification consistent with the evolution of a role in disease resistance for an uncharacterized family of plant genes. These findings highlight PADRE genes as prime candidates for the functional dissection of mechanisms underlying plant disease resistance to fungi.

Aspergillus alliaceus infection fatally shifts Orobanche hormones and phenolic metabolism

In this study, the physio pathological effects of Aspergillus alliaceus (Aa, fungi, biocontrol agent) on Orobanche (parasitic plant) were investigated by hormone and phenolic substance tests. In experimental group, Orobanches were treated with the fungi, considering control group was fungus-free. Based on the hormonal tests, in the experimental group, salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA) levels significantly decreased, and only indole acetic acid (IAA) hormone levels were fairly higher than the control group. According to phenolic substance tests, it was found that only gallic acid, syringic acid and caffeic acid values significantly increased compared with control, and catechin and p-coumaric acid values were significantly lower. Consequently, it was determined that Aa pathogenesis (1) considerably reduces the effects of all defence hormones (JA, ABA, SA), (2) operates an inadequate defence based solely on the IAA hormone and several phenolic substances (gallic acid, syringic acid and caffeic acid), (3) and inevitably the fungi lead the Orobanche to a slow and continuous death. The results were evaluated in detail in the light of similar recent article and current literature in terms of biocontrol and pathology.

The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation

Research into the relationship between epigenetic regulation and resistance to biotic stresses provides alternatives for plant protection and crop improvement. To unravel the mechanisms underlying tomato responses to Botrytis cinerea, we performed a chromatin immunoprecipitation (ChIP) analysis showing the increase in H3K9ac mark along the early induced genes SlyDES, SlyDOX1, and SlyLoxD encoding oxylipin-pathway enzymes, and SlyWRKY75 coding for a transcriptional regulator of hormonal signaling. This histone mark showed a more distinct distribution than the previously studied H3K4me3. The RNAPol-ChIP analysis reflected the actual gene transcription associated with increased histone modifications. A different pattern of marks in the oxylipin-related genes against P. syringae supported a pathogen-specific profile, while no significant differences occurred in SlyWRKY75. The epigenetic regulation of SlyWRKY75 by the intron-binding miR1127-3p was supported by the presence of SlyWRKY75 pre-mRNA in control plants. Interestingly, mRNA was found to be accumulated in response to B. cinerea and P. syringae, while reduction in miRNA only occurred against B. cinerea. The intronic region presented a similar pattern of marks than the rest of the gene in both pathosystems, except for H3K4me3 in the miRNA binding site upon B. cinerea. We located the gene encoding Sly-miR1127-3p, which presented reduced H3K4me3 on its promoter against B. cinerea.

Double-Stranded RNAs (dsRNAs) as a Sustainable Tool against Gray Mold (Botrytis cinerea) in Grapevine: Effectiveness of Different Application Methods in an Open-Air Environment

Grapevine is one of the most important and globally widespread fruit species, with a high impact on the economy of many countries but with an intense environmental effect. Therefore, new environmentally friendly defense strategies against fungal pathogens are needed for more sustainable agriculture. A novel emerging approach is spray-induced gene silencing (SIGS), which concerns the exogenous application of double-stranded RNA (dsRNA) inducing enhanced plant resistance against fungal pathogens. Here, we tested the ability of SIGS to prevent and counteract infection of Botrytis cinerea, one of the most economically impacting pathogens of grapevine. In particular, we tested three independent approaches for dsRNA delivery into plants: (i) high pressure spraying of leaves; (ii) petiole adsorption of dsRNAs; (iii) postharvest spraying of bunches. We demonstrated that independently from the method of application, SIGS can reduce virulence of the fungus. Moreover, we also observed three different levels of efficacy depending on the method of application. Thus, the present data provide crucial information on the possibility to exploit SIGS as an alternative sustainable and ecofriendly strategy for grapevine pre- and postharvest protection.

Stripe rust induced defence mechanisms in the leaves of contrasting barley genotypes (Hordeum vulgare L.) at the seedling stage

Puccinia striiformis f. sp. hordei, the causal organism of stripe rust in barley poses serious threats to its production. The present study examined the seedling response and changes in antioxidant defence system along with NADPH oxidase, hydrogen peroxide, and lipid peroxidation marker-malondialdehyde (MDA) in the four barley genotypes namely Jyoti, RD2900, RD2901, and RD2552 in response to M and G-races of stripe rust pathogen. Disease reaction showed Jyoti as susceptible genotype, RD2901 and RD2552 as resistant, whereas RD2900 behaved differentially to both the races. M-race which is predominant was found to be more virulent than G-race of barley stripe rust pathogen. RD2901 showed an increase in activities of NADPH oxidase, catalase, peroxidase, and enzymes of ascorbate-glutathione pathway along with ascorbate and glutathione pool on inoculation with M-race, which was accompanied by the decrease in hydrogen peroxide and MDA contents. Jyoti, on the other hand, showed an increase in peroxidase and glutathione-S-transferase activities only which were unable to maintain redox homeostasis. The scrutiny of data indicated an increase in ASA/DHA ratio on infection in all the genotypes irrespective of their behaviour towards the races. However, GSH/GSSG ratio significantly declined in Jyoti and increased or remained unaffected in the resistant genotypes which suggested that GSH/GSSG might be playing a vital role in imparting tolerance against stripe rust. Further, correlation studies also revealed that leaf damage was positively correlated with H₂O₂ and MDA contents.

Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis

Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in Arabidopsis thaliana, Meta-Analysis was employed with 257 publicly available Arabidopsis thaliana RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.

The host generalist phytopathogenic fungus Sclerotinia sclerotiorum differentially expresses multiple metabolic enzymes on two different plant hosts

Sclerotinia sclerotiorum is a necrotrophic fungal pathogen that infects upwards of 400 plant species, including several economically important crops. The molecular processes that underpin broad host range necrotrophy are not fully understood. This study used RNA sequencing to assess whether S. sclerotiorum genes are differentially expressed in response to infection of the two different host crops canola (Brassica napus) and lupin (Lupinus angustifolius). A total of 10,864 of the 11,130 genes in the S. sclerotiorum genome were expressed. Of these, 628 were upregulated in planta relative to in vitro on at least one host, suggesting involvement in the broader infection process. Among these genes were predicted carbohydrate-active enzymes (CAZYmes) and secondary metabolites. A considerably smaller group of 53 genes were differentially expressed between the two plant hosts. Of these host-specific genes, only six were either CAZymes, secondary metabolites or putative effectors. The remaining genes represented a diverse range of functional categories, including several associated with the metabolism and efflux of xenobiotic compounds, such as cytochrome P450s, metal-beta-lactamases, tannases and major facilitator superfamily transporters. These results suggest that S. sclerotiorum may regulate the expression of detoxification-related genes in response to phytotoxins produced by the different host species. To date, this is the first comparative whole transcriptome analysis of S. sclerotiorum during infection of different hosts.

Suppression of abscisic acid biosynthesis at the early infection stage of Verticillium longisporum in oilseed rape (Brassica napus)

Verticillium longisporum infects oilseed rape (Brassica napus) and Arabidopsis thaliana. To investigate the early response of oilseed rape to the fungal infection, we determined transcriptomic changes in oilseed rape roots at 6 days post-inoculation (dpi) by RNA-Seq analysis, in which non-infected roots served as a control. Strikingly, a subset of genes involved in abscisic acid (ABA) biosynthesis was found to be down-regulated and the ABA level was accordingly attenuated in 6 dpi oilseed rape as compared with the control. Gene expression analysis revealed that this was mainly attributed to the suppression of BnNCED3-mediated ABA biosynthesis, involving, for example, BnWRKY57. However, this down-regulation of ABA biosynthesis could not be observed in infected Arabidopsis roots. Arabidopsis ABA- defective mutants nced3 and aao3 displayed pronounced tolerance to the fungal infection with delayed and impeded symptom development, even though fungal colonization was not affected in both mutants. These data suggest that ABA appears to be required for full susceptibility of Arabidopsis to the fungal infection. Furthermore, we found that in both 6 dpi oilseed rape and the Arabidopsis nced3 mutant, the salicylic acid (SA) signalling pathway was induced while the jasmonic acid (JA)/ethylene (ET) signalling pathway was concomitantly mitigated. Following these data, we conclude that in oilseed rape the V. longisporum infection triggers a host-specific suppression of the NCED3-mediated ABA biosynthesis, consequently increasing plant tolerance to the fungal infection. We believe that this might be part of the virulence strategy of V. longisporum to initiate/establish a long-lasting compatible interaction with oilseed rape (coexistence), which appears to be different from the infection process in Arabidopsis.

The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations

The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mould management, while suggesting spatial optimization of crop organization within agricultural landscapes.

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

Fungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host mRNAs through complementary base pairing and suppress plant immunity. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for the production of sRNAs by S. sclerotiorum during infection is lacking. We sequenced sRNAs produced by S. sclerotiorum in vitro and during infection of two host species, Arabidopsis thaliana and Phaseolus vulgaris. We found that S. sclerotiorum produces at least 374 distinct highly abundant sRNAs during infection, mostly originating from repeat-rich plastic genomic regions. We predicted the targets of these sRNAs in A. thaliana and found that these genes were significantly more down-regulated during infection than the rest of the genome. Predicted targets of S. sclerotiorum sRNAs in A. thaliana were enriched for functional domains associated with plant immunity and were more strongly associated with quantitative disease resistance in a genome-wide association study (GWAS) than the rest of the genome. Mutants in A. thaliana predicted sRNA target genes SERK2 and SNAK2 were more susceptible to S. sclerotiorum than wild-type, suggesting that S. sclerotiorum sRNAs may contribute to the silencing of immune components in plants. The prediction of fungal sRNA targets in plant genomes can be combined with other global approaches, such as GWAS, to assist in the identification of plant genes involved in quantitative disease resistance.

Stimulatory Effects of Sublethal Doses of Carbendazim on the Virulence and Sclerotial Production of Botrytis cinerea

Stimulatory effects of low doses of fungicides on the virulence of phytopathogens have profound implications for applications of fungicides. The present study demonstrated that carbendazim sprayed at 0.001 to 0.03 μg/ml had stimulatory effects on the virulence of mycelia of Botrytis cinerea, and the maximum percent stimulations were 15.5 and 21.4% for isolates HB459 and HB536, respectively. Potato dextrose agar (PDA) amended with carbendazim at 0.01, 0.02, and 0.05 μg/ml inhibited mycelial growth of isolate HB536 by 0.8, 10.0, and 30.6%, respectively. However, after the inhibited mycelia were inoculated on cucumber leaves, virulence increased by 10.1, 12.9, and 10.8%, respectively. With respect to sclerotial production, carbendazim at 0.005 and 0.02 μg/ml in PDA significantly (P < 0.05) increased, while at 0.1 μg/ml significantly (P < 0.05) reduced the sclerotial number and weight of both isolates compared with nontreated controls. Conidia germination percentages slightly yet statistically significantly (P < 0.05) increased after being inoculated on PDA amended with carbendazim at 0.001 and 0.005 μg/ml. Carbendazim at 0.001∼0.02 μg/ml, either sprayed on cucumber leaves or cosuspended with conidia, exerted significantly (P < 0.05) stimulatory effects on the virulence of B. cinerea conidia. Mechanism studies showed that sublethal doses of carbendazim did not increase the expression levels of pathogenicity-related pectin methylesterase gene Bcpme1, endopolygalacturonase gene Bcpg2, cutinase gene CutA, xylanase gene Xyn11A, or NADPH oxidase gene BcnoxA.

Expression polymorphism at the ARPC4 locus links the actin cytoskeleton with quantitative disease resistance to Sclerotinia sclerotiorum in Arabidopsis thaliana

Quantitative disease resistance (QDR) is a form of plant immunity widespread in nature, and the only one active against broad host range fungal pathogens. The genetic determinants of QDR are complex and largely unknown, and are thought to rely partly on genes controlling plant morphology and development. We used genome-wide association mapping in Arabidopsis thaliana to identify ARPC4 as associated with QDR against the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Mutants impaired in ARPC4 showed enhanced susceptibility to S. sclerotiorum, defects in the structure of the actin filaments and in their responsiveness to S. sclerotiorum. Disruption of ARPC4 also alters callose deposition and the expression of defense-related genes upon S. sclerotiorum infection. Analysis of ARPC4 diversity in A. thaliana identified one haplotype (ARPC4^R ) showing a c. 1 kbp insertion in ARPC4 regulatory region and associated with higher level of QDR. Accessions from the ARPC4^R haplotype showed enhanced ARPC4 expression upon S. sclerotiorum challenge, indicating that polymorphisms in ARPC4 regulatory region are associated with enhanced QDR. This work identifies a novel actor of plant QDR against a fungal pathogen and provides a prime example of genetic mechanisms leading to the recruitment of cell morphology processes in plant immunity.

Intercellular cooperation in a fungal plant pathogen facilitates host colonization

Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.

Hormetic Effects of Mixtures of Carbendazim and Iprodione on the Virulence of Botrytis cinerea

Hormetic effects of fungicides on mycelial growth and virulence of plant pathogenic fungi have been reported, but the effects of fungicide mixtures on virulence hormesis of plant pathogens remain to be investigated. In this study, hormetic effects of mixtures of carbendazim and iprodione on the virulence of two carbendazim-resistant isolates of Botrytis cinerea were determined. Spraying carbendazim alone at 3 to 800 μg/ml exhibited hormetic effects on virulence to cucumber leaves, and carbendazim at 10 μg/ml had the maximum stimulation of 16.7% for isolate HBtom451. Spraying iprodione alone at 0.0001 to 0.0625 μg/ml exhibited hormetic effects on virulence, and iprodione at 0.025 μg/ml had the maximum stimulation of 18.7% for isolate HBtom451. However, spraying simultaneously carbendazim at 800 μg/ml and iprodione at 0.0625 μg/ml showed inhibitory effects on virulence to cucumber leaves. The mixture of carbendazim at 3 μg/ml and iprodione at 0.0001 μg/ml had much higher virulence stimulations than either fungicide at the same concentration alone. The maximum stimulation for the mixtures occurred at 10 and 0.0005 μg/ml for carbendazim and iprodione, respectively, and these concentrations were much lower than the concentration of their respective fungicide alone eliciting the maximum stimulations. The maximum stimulation amplitude for the mixture was slightly higher than that of each fungicide alone. These results demonstrated that carbendazim and iprodione mainly had dose-additive rather than amplitude-additive interactions when sprayed simultaneously with regard to virulence stimulations. Studies on virulence stimulations for mycelia treated with fungicide in potato dextrose agar showed that the maximum stimulation for the mixtures occurred at concentrations much lower than the concentration of carbendazim alone, indicating a dose-additive interaction when compared with carbendazim hormesis. Studies on potential physiological mechanisms of hormesis showed that increased tolerance to H₂O₂ may be one of the mechanisms for virulence hormesis for the mixtures of iprodione and carbendazim. These studies will advance our understanding of hormesis of fungicide mixtures.

Mechanisms of Broad Host Range Necrotrophic Pathogenesis in Sclerotinia sclerotiorum

Among necrotrophic fungi, Sclerotinia sclerotiorum is remarkable for its extremely broad host range and for its aggressive host tissue colonization. With full genome sequencing, transcriptomic analyses and the increasing pace of functional gene characterization, the factors underlying the basis of this broad host range necrotrophic pathogenesis are now being elucidated at a greater pace. Among these, genes have been characterized that are required for infection via compound appressoria in addition to genes associated with colonization that regulate oxalic acid (OA) production and OA catabolism. Moreover, virulence-related secretory proteins have been identified, among which are candidates for manipulating host activities apoplastically and cytoplasmically. Coupled with these mechanistic studies, cytological observations of the colonization process have blurred the heretofore clear-cut biotroph versus necrotroph boundary. In this review, we reexamine the cytology of S. sclerotiorum infection and put more recent molecular and genomic data into the context of this cytology. We propose a two-phase infection model in which the pathogen first evades, counteracts and subverts host basal defense reactions prior to killing and degrading host cells. Spatially, the pathogen may achieve this via the production of compatibility factors/effectors in compound appressoria, bulbous subcuticular hyphae, and primary invasive hyphae. By examining the nuances of this interaction, we hope to illuminate new classes of factors as targets to improve our understanding of broad host range necrotrophic pathogens and provide the basis for understanding corresponding host resistance.

Role of Phytohormones in Piriformospora indica-Induced Growth Promotion and Stress Tolerance in Plants: More Questions Than Answers

Phytohormones play vital roles in the growth and development of plants as well as in interactions of plants with microbes such as endophytic fungi. The endophytic root-colonizing fungus Piriformospora indica promotes plant growth and performance, increases resistance of colonized plants to pathogens, insects and abiotic stress. Here, we discuss the roles of the phytohormones (auxins, cytokinin, gibberellins, abscisic acid, ethylene, salicylic acid, jasmonates, and brassinosteroids) in the interaction of P. indica with higher plant species, and compare available data with those from other (beneficial) microorganisms interacting with roots. Crosstalks between different hormones in balancing the plant responses to microbial signals is an emerging topic in current research. Furthermore, phytohormones play crucial roles in systemic signal propagation as well as interplant communication. P. indica interferes with plant hormone synthesis and signaling to stimulate growth, flowering time, differentiation and local and systemic immune responses. Plants adjust their hormone levels in the roots in response to the microbes to control colonization and fungal propagation. The available information on the roles of phytohormones in beneficial root-microbe interactions opens new questions of how P. indica manipulates the plant hormone metabolism to promote the benefits for both partners in the symbiosis.