Molecular Mechanisms Underlying Fungicide Resistance in Citrus Postharvest Green Mold

Transcriptome Analysis Reveals Potential Regulators of DMI Fungicide Resistance in the Citrus Postharvest Pathogen Penicillium digitatum

Green mold, caused by Penicillium digitatum, is the major cause of citrus postharvest decay. Currently, the application of sterol demethylation inhibitor (DMI) fungicide is one of the main control measures to prevent green mold. However, the fungicide-resistance problem in the pathogen P. digitatum is growing. The regulatory mechanism of DMI fungicide resistance in P. digitatum is poorly understood. Here, we first performed transcriptomic analysis of the P. digitatum strain Pdw03 treated with imazalil (IMZ) for 2 and 12 h. A total of 1338 genes were up-regulated and 1635 were down-regulated under IMZ treatment for 2 h compared to control while 1700 were up-regulated and 1661 down-regulated under IMZ treatment for 12 h. The expression of about half of the genes in the ergosterol biosynthesis pathway was affected during IMZ stress. Further analysis identified that 84 of 320 transcription factors (TFs) were differentially expressed at both conditions, making them potential regulators in DMI resistance. To confirm their roles, three differentially expressed TFs were selected to generate disruption mutants using the CRISPR/Cas9 technology. The results showed that two of them had no response to IMZ stress while ∆PdflbC was more sensitive compared with the wild type. However, disruption of PdflbC did not affect the ergosterol content. The defect in IMZ sensitivity of ∆PdflbC was restored by genetic complementation of the mutant with a functional copy of PdflbC. Taken together, our results offer a rich source of information to identify novel regulators in DMI resistance.

Discovery and Transcriptional Profiling of Penicillium digitatum Genes That Could Promote Fungal Virulence during Citrus Fruit Infection

Green mold caused by Penicillium digitatum (Pers.:Fr.) Sacc is the most prevalent postharvest rot concerning citrus fruits. Using the subtractive suppression hybridization (SSH) technique, different P. digitatum genes have been identified that could be involved in virulence during citrus infection in the early stages, a crucial moment that determines whether the infection progresses or not. To this end, a comparison of two P. digitatum strains with high and low virulence has been carried out. We conducted a study on the gene expression profile of the most relevant genes. The results indicate the importance of transcription and regulation processes as well as enzymes involved in the degradation of the plant cell wall. The most represented expressed sequence tag (EST) was identified as PDIP_11000, associated with the FluG domain, which is putatively involved in the activation of conidiation. It is also worth noting that PDIP_02280 encodes a pectin methyl esterase, a cell wall remodeling protein with a high expression level in the most virulent fungal strains, which is notably induced during citrus infection. Furthermore, within the group with the greatest representation and showing significant induction in the early stages of infection, regulatory proteins (PDIP_68700, PDIP_76160) and a chaperone (PDIP_38040) stand out. To a lesser extent, but not less relevant, it is worth distinguishing different regulatory proteins and transcription factors, such as PDIP_00580, PDIP_49640 and PDIP_78930.

Comprehensive antifungal investigation of green synthesized silver nanoformulation against four agriculturally significant fungi and its cytotoxic applications

The present study reports the green synthesis of silver nanoparticles (AgNPs) in powder form using the leaf extract of Azadirachta indica. The synthesis of AgNPs was confirmed by UV-vis spectroscopy, FTIR, XRD, FESEM, and EDX. The synthesized AgNPs were in a powdered state and dispersed completely in 5% polyethylene glycol (PEG) and demonstrated prolonged shelf life and enhanced bioavailability over a year without any aggregation. The resulting silver nanoformulation demonstrated complete inhibition against Sclerotinia sclerotiorum and Colletotrichum falcatum and 68% to 80% inhibition against Colletotrichum gloeosporioides and Rhizoctonia solani respectively, at 2000 ppm. The EC50 values determined through a statistical analysis were 66.42, 157.7, 19.06, and 33.30 ppm for S. sclerotiorum, C. falcatum, C. gloeosporioides, and R. solani respectively. The silver nanoformulation also established significant cytotoxicity, with a 74.96% inhibition rate against the human glioblastoma cell line U87MG at 250 ppm. The IC50 value for the cancerous cell lines was determined to be 56.87 ppm through statistical analysis. The proposed silver nanoformulation may be used as a next-generation fungicide in crop improvement and may also find application in anticancer investigations. To the best of our knowledge, this is also the first report of silver nanoformulation demonstrating complete inhibition against the economically significant phytopathogen C. falcatum.

Essential oils on the control of fungi causing postharvest diseases in mango

The use of fungicides in the postharvest treatment of mangoes has been widespread due to the incidence of pathogens, but awareness of the health risks arising from their use has increased, driving the search for more sustainable treatments. This study aimed to evaluate the activity of antifungal treatment of seven essential oils (EO) against four fungi that cause postharvest diseases in mangoes and define the minimum inhibitory concentration (MIC) and chemical composition, analyzed by gas chromatography (GC-MS). The results showed that the EOs of oregano, rosemary pepper, cinnamon bark, and clove inhibited 100% of the mycelial growth of the studied pathogens, with MIC ranging from 250 to 2000 μL.L-1. The main compound found in oregano was carvacrol (69.1%); in rosemary and pepper oil, it was thymol (77.2%); cinnamaldehyde (85.1%) was the main constituent of cinnamon bark, and the eugenol (84.84%) in cloves. When evaluating the antifungal activity of these compounds, thymol and carvacrol showed greater inhibitory activity against fungi. Therefore, this study showed the great potential of oregano, clove, rosemary pepper, and cinnamon bark essential oil as alternative treatments to synthetic fungicides in controlling postharvest diseases in mangoes.

Carvacrol Encapsulation in Chitosan-Carboxymethylcellulose-Alginate Nanocarriers for Postharvest Tomato Protection

Advancements in polymer science and nanotechnology hold significant potential for addressing the increasing demands of food security, by enhancing the shelf life, barrier properties, and nutritional quality of harvested fruits and vegetables. In this context, biopolymer-based delivery systems present themselves as a promising strategy for encapsulating bioactive compounds, improving their absorption, stability, and functionality. This study provides an exploration of the synthesis, characterization, and postharvest protection applications of nanocarriers formed through the complexation of chitosan oligomers, carboxymethylcellulose, and alginate in a 2:2:1 molar ratio. This complexation process was facilitated by methacrylic anhydride and sodium tripolyphosphate as cross-linking agents. Characterization techniques employed include transmission electron microscopy, energy-dispersive X-ray spectroscopy, infrared spectroscopy, thermal analysis, and X-ray powder diffraction. The resulting hollow nanospheres, characterized by a monodisperse distribution and a mean diameter of 114 nm, exhibited efficient encapsulation of carvacrol, with a loading capacity of approximately 20%. Their suitability for phytopathogen control was assessed in vitro against three phytopathogens-Botrytis cinerea, Penicillium expansum, and Colletotrichum coccodes-revealing minimum inhibitory concentrations ranging from 23.3 to 31.3 μg·mL-1. This indicates a higher activity compared to non-encapsulated conventional fungicides. In ex situ tests for tomato (cv. 'Daniela') protection, higher doses (50-100 μg·mL-1, depending on the pathogen) were necessary to achieve high protection. Nevertheless, these doses remained practical for real-world applicability. The advantages of safety, coupled with the potential for a multi-target mode of action, further enhance the appeal of these nanocarriers.

Fatty acid metabolism and C9 aldehyde biosynthesis are involved in ε-poly-l-lysine-induced citrus fruit resistance to Penicillium digitatum

Citrus fruit were easily infected by Penicillium digitatum, and caused green mold rapidly, resulting in enormous post-harvest losses. ε-poly-l-lysine (ε-PL) was generally regarded as a safe (GRAS) substance. Besides, it was proved to have a dual effect on harming fungi and triggering fruit defense responses. Fatty acid metabolism is closely related to fruit defense response. However, little is known about how ε-PL affected fatty acid metabolism in citrus fruit. Here, we found that ε-PL increased the expression of CsFATA, CsACSL, CsFAD2, CsFAD3, CsLOX2S, and CsHPL in fatty acid metabolism, decreasing oleic acid levels and enhancing linoleic and linolenic acid levels. Additionally, ε-PL enriched the activities of LOX and HPL during the oxidative decomposition of fatty acids, and activating C9 aldehyde biosynthesis. Interestingly, ε-PL combined with (2E,4E)-nonadienal (C9 aldehyde) would improve the inhibitory effect against Penicillium digitatum. And the combined bio-fungicide significantly delayed the citrus green mold compared to single concentrations of the individual components. These results suggested that ε-PL improved citrus fruit defense responses through fatty acid-mediated defense responses. Combined bio-fungicide consisting of ε-PL and (2E,4E)-nonadienal have an excellent prospect for controlling citrus green mold.

Application of Thymol Vapors to Control Postharvest Decay Caused by Penicillium digitatum and Lasiodiplodia theobromae in Grapefruit

Two of the major postharvest diseases impacting grapefruit shelf life and marketability in the state of Florida (USA) are stem-end rot (SER) caused by Lasiodiplodia theobromae and green mold (GM) caused by Penicillium digitatum. Here, we investigated the in vitro and in vivo efficacy of vapors of thymol, a natural compound found in the essential oil of various plants and the primary constituent of thyme (Thymus vulgaris) oil, as a potential solution for the management of GM and SER. Thymol vapors at concentrations lower than 10 mg L-1 significantly inhibited the mycelial growth of both pathogens, causing severe ultrastructural damage to P. digitatum conidia. In in vivo trials, the incidence and lesion area of GM and SER on inoculated grapefruit were significantly reduced after a 5 d exposure to 50 mg L-1 thymol vapors. In addition, the in vitro and in vivo sporulation of P. digitatum was suppressed by thymol. When applied in its vapor phase, thymol had no negative effect on the fruit, neither introducing perceivable off-flavor nor causing additional weight loss. Our findings support the pursuit of further studies on the use of thymol, recognized as safe for human health and the environment, as a promising strategy for grapefruit postharvest disease management.

Random amplified microsatellites (RAMS) analysis ascertains genetic variation of Alternaria alternata causing black spot disease on Carya illinoinensis in South Africa

Limited information regarding the occurrence of black spot disease of pecan (Carya illinoinensis), caused by A. alternata, in South Africa is known. The pecan industry is growing rapidly, so it is essential to understand the impact of the fungal pathogen to pecan health. In this study, the genetic variation of 364 A. alternata isolates was investigated by two RAMS primers (CCA5 and CGA5). In total, 6,525 alleles were produced, with a minimum of 3,182 alleles on the CGA5 primer and maximum of 3,343 alleles for CCA5 primer. Further analysis of the primers showed relatively low genetic diversity of A. alternata isolate populations, with mean values; (H = 0.12) and Shannon's information index (I = 0.20). The analysis of molecular variance (AMOVA) revealed significant differences between populations, with 88% of the genetic variation was found within populations (Nm = 3.59, PhiPT = 0.12), and were not significantly different (p > 0.001). While 12% variation was observed among populations (Nm = 2.89, PhiPT = 0.08) and the estimates were statistically significant (p < 0.001). STRUCTURE HARVESTER output showed that K value is K = 8, where ΔK cannot find the true number of populations because of less variation. The dendrogram cluster tree generated by Ward's analysis unveiled two main distinct clades and 10 sub-clades, revealing similar findings as those of PCoA analysis clusters. Therefore, it was evident that these analyses depicted no distinct relationship between the A. alternata isolates and their geographic locations or the prevalence of distribution among the populations.

Efficient control of the fungal pathogens Colletotrichum gloeosporioides and Penicillium digitatum infecting citrus fruits by native soilborne Bacillus velezensis strains

Destruction of citrus fruits by fungal pathogens during preharvest and postharvest stages can result in severe losses for the citrus industry. Antagonistic microorganisms used as biological agents to control citrus pathogens are considered alternatives to synthetic fungicides. In this study, we aimed to identify fungal pathogens causing dominant diseases on citrus fruits in a specialized citrus cultivation region of Vietnam and inspect soilborne Bacillus isolates with antifungal activity against these pathogens. Two fungal pathogens were characterized as Colletotrichum gloeosporioides and Penicillium digitatum based on morphological characteristics and ribosomal DNA internal transcribed spacer sequence analyses. Reinfection assays of orange fruits confirmed that C. gloeosporioides causes stem-end rot, and P. digitatum triggers green mold disease. By the heterologous expression of the green fluorescent protein (GFP) in C. gloeosporioides using Agrobacterium tumefaciens-mediated transformation, we could observe the fungal infection process of the citrus fruit stem-end rot caused by C. gloeosporioides for the first time. Furthermore, we isolated and selected two soilborne Bacillus strains with strong antagonistic activity for preventing the decay of citrus fruits by these pathogens. Molecular analyses of 16 S rRNA and gyrB genes showed that both isolates belong to B. velezensis. Antifungal activity assays indicated that bacterial culture suspensions could strongly inhibit C. gloeosporioides and P. digitatum, and shield orange fruits from the invasion of the pathogens. Our work provides a highly effective Bacillus-based preservative solution for combating the fungal pathogens C. gloeosporioides and P. digitatum to protect citrus fruits at the postharvest stages.

Biotechnology approaches to reduce antimicrobial resistant postharvest pathogens, mycotoxin contamination, and resulting product losses

Postharvest fungal pathogens of stored fruits, nuts, and vegetables cause food spoilage and some produce mycotoxins that harm human health. These fungi can develop resistance to the chemicals used for their control despite judicious use, rotating different chemistries, and routine resistance monitoring. Once antimicrobial resistance develops, these fungi are difficult to control and persist in the field, packing, and storage environments. Therefore, new tools and approaches for control with reduced emphasis on chemicals and movement toward durable, innovative approaches (e.g. double-stranded RNA, translational metagenomics, and host-induced gene silencing) are warranted. The focus of this review is on formative breakthroughs to combat postharvest pathogens and the mycotoxins they produce via translation of fundamental science using biotechnology tools.

Biochemical and genetic characterization of Botrytis cinerea laboratory mutants resistant to propamidine

BACKGROUND

Botrytis cinerea, the causal agent of gray mold, is one of the top 10 fungal pathogens in the world. Propamidine, an aromatic diamidine compound, exhibited both protective and therapeutic effects against B. cinerea. However, the resistance risk and mechanism of B. cinerea to propamidine are unclear.

RESULTS

Twelve high and stable resistant mutants were obtained from B. cinerea B05.10 by fungicide induction. Compared with the parental strain, the biological fitness of the mutants, including growth rate, spore germination, pathogenicity, and oxalic acid decreased significantly. There was no cross-resistance among propamidine and other commonly used fungicides, while the efficacy of propamidine against the resistance mutants declined. In addition, the cell membrane permeability, substance metabolism, and defense enzyme activities of the resistant mutants were significantly increased compared with the wild strain. Whole-genome sequencing of all resistant mutants found that there were 32 SNPs and nine InDels. Importantly, nine common single-point mutant genes in the exon region were found in all 12 resistant mutants, and these genes were related to multiple pathways in vivo, indicating that many factors contributed to the formation of propamidine resistance.

CONCLUSION

These data suggested the resistance risk of B. cinerea to propamidine was low to moderate and the mechanism of propamidine was different from that of the existing fungicides. These results will increase understanding of the resistance mechanism of propamidine and provide a critical basis for the rational design of pesticide molecules based on targets. © 2022 Society of Chemical Industry.

γ-Cyclodextrin-Encapsulated Cinnamaldehyde for Citrus Preservation and Its Potential Mechanisms against Penicillium digitatum

In this study, a γ-cyclodextrin-cinnamaldehyde inclusion compound (γ-CDCL) was prepared to control green mold caused by Penicillium digitatum (P. digitatum) in citrus. The results showed that the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of γ-CDCL against the mycelial growth of P. digitatum were 2.0 g L−1 and 4.0 g L−1, respectively. Simultaneously, eight × MFC γ-CDCL could effectively reduce the incidence of green mold in citrus fruit without impairment of the fruit qualities, meanwhile, eight × MFC γ-CDCL was comparable to Prochloraz in controlling fruit under natural storage conditions. The structure of γ-CDCL was characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform-infrared spectroscopy (FT-IR), and nuclear magnetic resonance (NMR) analyses. Results showed that the successful preparation of γ-CDCL was due to the spatial interaction between H-4,8 of cinnamaldehyde and H-5′ of γ-cyclodextrin. Meanwhile, the cell membrane permeability of P. digitatum was impaired by γ-CDCL through massive accumulation of reactive oxygen species, whereas the cell wall integrity was barely affected. These results indicated that γ-CDCL might inhibit the growth of P. digitatum through a membrane damage mechanism and it is a promising alternative to chemical fungicides in controlling the post-harvest citrus decay.

Penicillium digitatum as a Model Fungus for Detecting Antifungal Activity of Botanicals: An Evaluation on Vietnamese Medicinal Plant Extracts

Medicinal plants play important roles in traditional medicine, and numerous compounds among them have been recognized for their antimicrobial activity. However, little is known about the potential of Vietnamese medicinal plants for antifungal activity. In this study, we examined the antagonistic activity of twelve medicinal plant species collected in Northern Vietnam against Penicillium digitatum, Aspergillus flavus, Aspergillus fumigatus, and Candida albicans. The results showed that the antifungal activities of the crude extracts from Mahonia bealei, Ficus semicordata, and Gnetum montanum were clearly detected with the citrus postharvest pathogen P. digitatum. These extracts could fully inhibit the growth of P. digitatum on the agar medium, and on the infected citrus fruits at concentrations of 300–1000 µg/mL. Meanwhile, the other tested fungi were less sensitive to the antagonistic activity of the plant extracts. In particular, we found that the ethanolic extract of M. bealei displayed a broad-spectrum antifungal activity against all four pathogenic fungi. Analysis of this crude extract by enrichment coupled with high-performance liquid chromatography revealed that berberine and palmatine are major metabolites. Additional inspections indicated berberine as the key compound responsible for the antifungal activity of the M. bealei ethanolic extract. Our study provides a better understanding of the potential of Vietnamese medicinal plant resources for combating fungal pathogens. This work also highlights that the citrus pathogen P. digitatum can be employed as a model fungus for screening the antifungal activity of botanicals.

Intracellular production of reactive oxygen species and a DAF-FM-related compound in Aspergillus fumigatus in response to antifungal agent exposure

Fungi are ubiquitously present in our living environment and are responsible for crop and infectious diseases. Developing new antifungal agents is constantly needed for their effective control. Here, we investigated fungal cellular responses to an array of antifungal compounds, including plant- and bacteria-derived antifungal compounds. The pathogenic fungus Aspergillus fumigatus generated reactive oxygen species in its hyphae after exposure to the antifungal compounds thymol, farnesol, citral, nerol, salicylic acid, phenazine-1-carbonic acid, and pyocyanin, as well as under oxidative and high-temperature stress conditions. The production of nitric oxide (NO) was determined using diaminofluorescein-FM diacetate (DAF-FM DA) and occurred in response to antifungal compounds and stress conditions. The application of reactive oxygen species or NO scavengers partly suppressed the inhibitory effects of farnesol on germination. However, NO production was not detected in the hyphae using the Greiss method. An LC/MS analysis also failed to detect DAF-FM-T, a theoretical product derived from DAF-FM DA and NO, in the hyphae after antifungal treatments. Thus, the cellular state after exposure to antifungal agents may be more complex than previously believed, and the role of NO in fungal cells needs to be investigated further.

Molecular Physicochemical Properties of Selected Pesticides as Predictive Factors for Oxidative Stress and Apoptosis-Dependent Cell Death in Caco-2 and HepG2 Cells

In this work, three pesticides of different physicochemical properties: glyphosate (GLY, herbicide), imidacloprid (IMD, insecticide), and imazalil (IMZ, fungicide), were selected to assess their cytotoxicity against Caco-2 and HepG2 cells. Cell viability was assessed by the Alamar Blue assay, after 24 and 48 h exposure to different concentrations, and IC50 values were calculated. The mechanisms underlying toxicity, namely cellular reactive oxygen species (ROS), glutathione (GSH) content, lipid peroxidation, loss of mitochondrial membrane potential (MMP), and apoptosis/necrosis induction were assessed by flow cytometry. Cytotoxic profiles were further correlated with the molecular physicochemical parameters of pesticides, namely: water solubility, partition coefficient in an n-octanol/water (Log Pow) system, topological polar surface area (TPSA), the number of hydrogen-bonds (donor/acceptor), and rotatable bonds. In vitro outputs resulted in the following toxicity level: IMZ (Caco-2: IC50 = 253.5 ± 3.37 μM, and HepG2: IC50 = 94 ± 12 μM) > IMD (Caco-2: IC50 > 1 mM and HepG2: IC50 = 624 ± 24 μM) > GLY (IC50 >>1 mM, both cell lines), after 24 h treatment, being toxicity time-dependent (lower IC50 values at 48 h). Toxicity is explained by oxidative stress, as IMZ induced a higher intracellular ROS increase and lipid peroxidation, followed by IMD, while GLY did not change these markers. However, the three pesticides induced loss of MMP in HepG2 cells while in Caco-2 cells only IMZ produced significant MMP loss. Increased ROS and loss of MMP promoted apoptosis in Caco-2 cells subjected to IMZ, and in HepG2 cells exposed to IMD and IMZ, as assessed by Annexin-V/PI. The toxicity profile of pesticides is directly correlated with their Log Pow, as affinity for the lipophilic environment favours interaction with cell membranes governs, and is inversely correlated with their TPSA; however, membrane permeation is favoured by lower TPSA. IMZ presents the best molecular properties for membrane interaction and cell permeation, i.e., higher Log Pow, lower TPSA and lower hydrogen-bond (H-bond) donor/acceptor correlating with its higher toxicity. In conclusion, molecular physicochemical factors such as Log Pow, TPSA, and H-bond are likely to be directly correlated with pesticide-induced toxicity, thus they are key factors to potentially predict the toxicity of other compounds.

In Vitro Assessment of Pesticides Toxicity and Data Correlation with Pesticides Physicochemical Properties for Prediction of Toxicity in Gastrointestinal and Skin Contact Exposure

In this work, three pesticides of different physicochemical properties, namely, glyphosate (herbicide), imidacloprid (insecticide) and imazalil (fungicide), were selected to assess their cytotoxicity against distinct cell models (Caco-2, HepG2, A431, HaCaT, SK-MEL-5 and RAW 264.7 cells) to mimic gastrointestinal and skin exposure with potential systemic effect. Cells were subjected to different concentrations of selected pesticides for 24 h or 48 h. Cell viability was assessed by Alamar Blue assay, morphological changes by bright-field microscopy and the IC50 values were calculated. Cytotoxic profiles were analysed using the physico-chemical parameters of the pesticides, namely: molecular weight, water solubility, the partition coefficient in the n-octanol/water (Log Pow) system, the topological polar surface area (TPSA), and number of hydrogen-bonds (donor/acceptor) and rotatable bonds. Results showed that glyphosate did not reduce cell viability (up to 1 mM), imidacloprid induced moderate toxicity (IC50 > 1 mM for Caco-2 cells while IC50 = 305.9 ± 22.4 μM for RAW 264.7 cells) and imazalil was highly cytotoxic (IC50 > 253.5 ± 3.37 for Caco-2 cells while IC50 = 31.3 ± 2.7 μM for RAW 264.7 cells) after 24 h exposure. Toxicity was time-dependent as IC50 values at 48 h exposure were lower, and decrease in cell viability was accompanied by changes in cell morphology. Pesticides toxicity was found to be directly proportional with their Log Pow, indicating that the affinity to a lipophilic environment such as the cell membranes governs their toxicity. Toxicity is inverse to pesticides TPSA, but lower TPSA favours membrane permeation. The lower toxicity against Caco-2 cells was attributed to the physiology and metabolism of cell barriers equipped with various ABC transporters. In conclusion, physicochemical factors such as Log Pow, TPSA and H-bond are likely to be directly correlated with pesticide-induced toxicity, thus being key factors to potentially predict the toxicity of other compounds.

Biocontrol Ability of the Bacillus amyloliquefaciens Group, B. amyloliquefaciens, B. velezensis, B. nakamurai, and B. siamensis, for the Management of Fungal Postharvest Diseases: A Review

The Bacillus amyloliquefaciens group, composed of B. amyloliquefaciens, B. velezensis, B. nakamurai, and B. siamensis, has recently emerged as an interesting source of biocontrol agents for the management of pathogenic fungi. In this review, all the reports regarding the ability of these species to control postharvest fungal diseases have been covered for the first time. B. amyloliquefaciens species showed various antifungal mechanisms, including production of antifungal lipopeptides and volatile organic compounds, competition for nutrients, and induction of disease resistance. Most reports discussed their use for the control of fruit diseases. Several strains were studied in combination with additives, improving their inhibitory efficacies. In addition, a few strains have been commercialized. Overall, studies showed that B. amyloliquefaciens species are a suitable environmentally friendly alternative for the control of postharvest diseases. However, there are still crucial knowledge gaps to improve their efficacy and host range.

The population genetics of adaptation through copy‐number variation in a fungal plant pathogen

Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell-wall-degrading enzymes). We perform genome-wide association studies (GWAS) and identify a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome-wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV-focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.

Deciphering Molecular Determinants Underlying Penicillium digitatum's Response to Biological and Chemical Antifungal Agents by Tandem Mass Tag (TMT)-Based High-Resolution LC-MS/MS

Penicillium digitatum is a widespread pathogen responsible for the postharvest decay of citrus, one of the most economically important crops worldwide. Currently, chemical fungicides are still the main strategy to control the green mould disease caused by the fungus. However, the increasing selection and proliferation of fungicide-resistant strains require more efforts to explore new alternatives acting via new or unexplored mechanisms for postharvest disease management. To date, several non-chemical compounds have been investigated for the control of fungal pathogens. In this scenario, understanding the molecular determinants underlying P. digitatum's response to biological and chemical antifungals may help in the development of safer and more effective non-chemical control methods. In this work, a proteomic approach based on isobaric labelling and a nanoLC tandem mass spectrometry approach was used to investigate molecular changes associated with P. digitatum's response to treatments with α-sarcin and beetin 27 (BE27), two proteins endowed with antifungal activity. The outcomes of treatments with these biological agents were then compared with those triggered by the commonly used chemical fungicide thiabendazole (TBZ). Our results showed that differentially expressed proteins mainly include cell wall-degrading enzymes, proteins involved in stress response, antioxidant and detoxification mechanisms and metabolic processes such as thiamine biosynthesis. Interestingly, specific modulations in response to protein toxins treatments were observed for a subset of proteins. Deciphering the inhibitory mechanisms of biofungicides and chemical compounds, together with understanding their effects on the fungal physiology, will provide a new direction for improving the efficacy of novel antifungal formulations and developing new control strategies.