A molecular mechanism of azoxystrobin resistance in Penicillium digitatum UV mutants and a PCR-based assay for detection of azoxystrobin-resistant strains in packing- or store-house isolates

Chlorophyllin and sunlight against Penicillium digitatum: exploring Photodynamic Inactivation as a green postharvest technology in citriculture

Green mold, induced by the fungal phytopathogen Penicillium digitatum, is one of the major causes of postharvest losses in citriculture. To minimize mold infections oranges are treated harshly with fungicides, edible coatings, or physical treatment, leading to evolving resistance, low consumer acceptance, or reduced crop quality, respectively. Photodynamic Inactivation (PDI) might represent an ecofriendly alternative for treatment of P. digitatum spoilage, especially if based on natural photosensitizers. Here, we introduce PDI using three formulations consisting of different concentrations of the natural photosensitizer sodium magnesium chlorophyllin (Chl), Na2EDTA as cell-wall permeabilizing agent and a surfactant for postharvest treatment of P. digitatum. As experimental model systems (i) mycelial spheres in liquid suspension, (ii) fungal spores or (iii) a newly developed experimental setup using orange peel plugs are employed. Illumination was done by an LED device with a main wavelength of 395 nm (106 J cm-2). The lowest concentrated photosensitizer formulation (219 µM Chl) effectively photokilled samples of model systems (i) and (ii) with 100% and 62.5% dead samples, respectively. Orange peel plugs of model system (iii) were best disinfected using the mid-concentrated formulation (475 µM Chl, 70% dead samples). Additionally, model systems (ii) and (iii) were treated with the mid-concentrated formulation and illuminated by sunlight. Eradication of P. digitatum liquid spore culture (ii) was enhanced when illuminating with sunlight (300 J cm-2). Further, a complete disinfection of orange peel plugs (iii, 100% dead samples) was achieved with sunlight (300 J cm-2). To evaluate the antioxidant scavenging activity post-PDI treatment with LED light (395 nm, 106 J cm-2) a DPPH assay was performed on model system (iii). The treatment with the mid- and low-concentrated Chl formulations and LED light showed little to no change in DPPH scavenging activity when compared to the not-illuminated controls. Concisely, with this study we demonstrate that PDI using Chl-based photosensitizer formulations has an in vitro antifungal effect against P. digitatum, without altering the antioxidant scavenging activity of the fruit. Different model systems, to mimic the different stages of green mold infection, were effectively treated with Chl and sunlight.

Biocontrol potential of Bacillus velezensis wr8 secondary metabolites against Penicillium sp

The aim of this study was to isolate and identify native Bacillus from citrus fruits, with inhibition phenotypes to Penicillium sp. We investigated the antifungal effect of Bacillus velezensis wr8 on the postharvest pathogens Penicillium sp. inoculated on fruits, as well as on the growth of these fungi on Petri dishes with defined media. MALDI-TOF MS was conducted to enlighten the underlying mechanism. Results showed that Bacillus velezensis wr8 significantly inhibited Penicillium sp. growth in vitro. Moreover, secondary metabolites suppressed the disease development of citrus fruits artificially inoculated with Penicillium sp. in 25 °C. Furthermore, MALDI-TOF MS indicated that lipoprotein with the molecular mass of 30.2 kDa was a key component about against Penicillium sp. In addition, the secondary metabolites with antibacterial activity against Escherichia coli showed antimicrobial peptide with the molecular weight of 9.8 kDa. These results demonstrated that Bacillus velezensis wr8 could produce lipoprotein and antimicrobial peptide to inhibit Penicillium sp. and Escherichia coli which has broad application prospect in the future development. Finally, Bacillus velezensis wr8 is to provide data support for the development and utilization of high activity bacteriocin at room temperature and its application in the field of food safety.

Development of a Method for Detecting and Estimating Moniliophthora roreri Spore Loads Based on Spore Traps and qPCR

Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America and, to better comprehend its epidemiology, we must understand its dissemination and proliferation. However, we do not know how M. roreri spores loads fluctuate in time and space due to the lack of a reliable technique to quantify M. roreri spores in the fields. Therefore, we developed a method that relies on spore traps and qPCR to detect and quantify M. roreri spore loads. This study demonstrated that the qPCR protocol can detect down to 0.025 ng of M. roreri DNA and quantify between 0.006 ng and 60 ng. Moreover, it demonstrated that qPCR protocol can detect and quantify DNA extracted from spore suspension and spore traps containing at least 2.9 × 104 M. roreri spores. However, the variability of the estimates for spore samples was high. Finally, we described a spore-trap device designed to carry spore traps in the field. The qPCR protocol and spore-trap device here developed will help in the understanding of the M. roreri dissemination patterns since they can be used to assess the environmental loads of M. roreri spore in cacao fields.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.

Study on the Infection Mechanism of Penicillium Digitatum on Postharvest Citrus (Citrus Reticulata Blanco) Based on Transcriptomics

Penicillium digitatum is one of the most important pathogens known widely to cause postharvest losses of citrus. It is significant to explore its infection mechanism to improve the control technology of postharvest diseases of citrus. This research aimed to study the changes in gene expression of P. digitatum at its early stages of citrus infection by transcriptomics sequencing and bioinformatics analysis in order to explore the molecular mechanism of its infection. The results showed that genes associated with pathogenic factors, such as cell wall degrading enzymes, ethylene, organic acids, and effectors, were significantly up-regulated. Concurrently, genes related to anti-oxidation and iron transport were equally up-regulated at varying degrees. From this study, we demonstrated a simple blueprint for the infection mechanism of P. digitatum in Citrus reticulata Blanco, which provided a new direction for subsequent pathological research and paves the way for developing new control strategies.

Elucidation of the Initial Growth Process and the Infection Mechanism of Penicillium digitatum on Postharvest Citrus (Citrus reticulata Blanco)

Green mold disease, a common citrus post-harvest disease caused by Penicillium digitatum, has an unresolved initial infection mechanism. Understanding the infection mechanism leads to the development of potential controls and preventive measures against the disease. The present study aimed to delineate the infection mechanism by investigating spore germination, changes of organic molecules and enzyme activity, and differential expression of genes in the P. digitatum infection. P. digitatum spore germination was observed by a pathology section scanner and it was found that in vivo germination was 3 h behind the in vitro germination. In addition, cell wall degrading enzymes and soluble sugar and titratable acid content during the infection process measured dynamically. The level of pectinase reached its maximum of 6067 U/g before 48 hpi, while cellulase increased rapidly after 48 hpi. The soluble sugar and organic acid content increased considerably with the progression of the infection. The transcriptomic profile of P. digitatum before and after infection was analyzed by RNA-seq. The genes related to cell wall degrading enzymes were significantly up-regulated and annotated to participate in two major carbon source synthesis pathways. The study delineated the initial infection mechanism of P. digitatum which eventually opened the gate way for the development of new control strategies in the future.

Cloning of the Cytochrome b Gene From the Tomato Powdery Mildew Fungus Leveillula taurica Reveals High Levels of Allelic Variation and Heteroplasmy for the G143A Mutation

Leveillula taurica is a major pathogen of tomato and several other crops that can cause substantial yield losses in favorable conditions for the fungus. Quinone outside inhibitor fungicides (Q_oIs) are routinely used for the control of the pathogen in tomato fields across California, but their recurrent use could lead to the emergence of resistance against these compounds. Here, we partially cloned the cytochrome b gene from L. taurica (Lt cytb) and searched within populations of the fungus collected from tomato fields across California for mutations that confer resistance to Q_oIs. A total of 21 single nucleotide polymorphisms (SNPs) were identified within a 704 bp fragment of the Lt cytb gene analyzed, of which five were non-synonymous substitutions. Among the most frequent SNPs encountered within field populations of the pathogen was the G143A substitution that confers high levels of resistance against Q_oIs in several fungi. The other four amino acid substitutions were novel mutations, whose effect on Q_oI resistance is currently unknown. Sequencing of the Lt cytb gene from individual single-cell conidia of the fungus further revealed that most SNPs, including the one leading to the G143A substitution, were present in a heteroplasmic state, indicating the co-existence of multiple mitotypes in single cells. Analysis of the field samples showed that the G143A substitution is predominantly heteroplasmic also within field populations of L. taurica in California, suggesting that Q_oI resistance in this fungus is likely to be quantitative rather than qualitative.

Biological and chemical diversity go hand in hand: Basidiomycota as source of new pharmaceuticals and agrochemicals

The Basidiomycota constitutes the second largest higher taxonomic group of the Fungi after the Ascomycota and comprises over 30.000 species. Mycelial cultures of Basidiomycota have already been studied since the 1950s for production of antibiotics and other beneficial secondary metabolites. Despite the fact that unique and selective compounds like pleuromutilin were obtained early on, it took several decades more until they were subjected to a systematic screening for antimicrobial and anticancer activities. These efforts led to the discovery of the strobilurins and several hundreds of further compounds that mainly constitute terpenoids. In parallel the traditional medicinal mushrooms of Asia were also studied intensively for metabolite production, aimed at finding new therapeutic agents for treatment of various diseases including metabolic disorders and the central nervous system. While the evaluation of this organism group has in general been more tedious as compared to the Ascomycota, the chances to discover new metabolites and to develop them further to candidates for drugs, agrochemicals and other products for the Life Science industry have substantially increased over the past decade. This is owing to the revolutionary developments in -OMICS techniques, bioinformatics, analytical chemistry and biotechnological process technology, which are steadily being developed further. On the other hand, the new developments in polythetic fungal taxonomy now also allow a more concise selection of previously untapped organisms. The current review is dedicated to summarize the state of the art and to give an outlook to further developments.

Heteroplasmy for the Cytochrome b Gene in Podosphaera xanthii and its Role in Resistance to QoI Fungicides in Spain

In Spain, management of the cucurbit powdery mildew pathogen Podosphaera xanthii is strongly dependent on chemicals such as quinone outside inhibitor (QoI) fungicides. In a previous report, widespread resistance to QoI fungicides in populations of P. xanthii in south-central Spain was documented, but the molecular mechanisms of resistance remained unclear. In this work, the role of the Rieske-FeS (risp) and the cytochrome b (cytb) gene mutations in QoI resistance of P. xanthii were examined. No point mutations in the risp gene were found in the three QoI-resistant isolates analyzed. For cytb, sequence analysis revealed the presence of a G143A substitution that occurs in many QoI-resistant fungi. This mutation was always detected in QoI-resistant isolates of P. xanthii; however, it was also detected in sensitive isolates. To better understand the role of heteroplasmy for cytb in QoI resistance of P. xanthii, an allele-specific quantitative PCR was developed to quantify the relative abundance of the G143 (sensitive) and A143 (resistant) alleles. High relative abundance of A143 allele (70%) was associated with isolates resistant to QoI fungicides; however, QoI-sensitive isolates also carried the mutated allele in frequencies ranged from 10 to 60%. Our data suggest that G143A mutation in cytb is the primary factor involved in QoI resistance of P. xanthii but the proportion of G143 and A143 alleles in an isolate may determine its QoI resistance level.

Functional analysis of two sterol regulatory element binding proteins in Penicillium digitatum

The sterol regulatory element binding proteins (SREBPs) are key regulators for sterol homeostasis in most fungi. In the citrus postharvest pathogen Penicillium digitatum, the SREBP homolog is required for fungicide resistance and regulation of CYP51 expression. In this study, we identified another SREBP transcription factor PdSreB in P. digitatum, and the biological functions of both SREBPs were characterized and compared. Inactivation of PdsreA, PdsreB or both genes in P. digitatum reduced ergosterol contents and increased sensitivities to sterol 14-α-demethylation inhibitors (DMIs) and cobalt chloride. Fungal strains impaired at PdsreA but not PdsreB increased sensitivity to tridemorph and an iron chelator 2,2'-dipyridyl. Virulence assays on citrus fruit revealed that fungal strains impaired at PdsreA, PdsreB or both induce maceration lesions similar to those induced by wild-type. However, ΔPdsreA, ΔPdsreB or the double mutant strain rarely produce aerial mycelia on infected citrus fruit peels. RNA-Seq analysis showed the broad regulatory functions of both SREBPs in biosynthesis, transmembrane transportation and stress responses. Our results provide new insights into the conserved and differentiated regulatory functions of SREBP homologs in plant pathogenic fungi.

Use of active extracts of poplar buds against Penicillium italicum and possible modes of action

Antifungal components, from poplar buds active fraction (PBAF) against Penicillium italicum, the causal agent of blue mold in citrus fruits, were identified and possible action modes were investigated. Pinocembrin, chrysin and galangin were determined as active components in PBAF, using HPLC and HPLC-MS analysis. The antifungal activity is stable at temperatures ranging from 4 °C to 100 °C and pH levels ranging from 4 to 8. In the presence of PBAF, the hyphae become shriveled, wrinkled and the cell membrane became seriously disrupted. Further investigation on cell permeability, nucleic acid content and alkaline phosphatase suggest that the cell membrane might be the target. Mycelial oxygen consumption and the respiration-related enzymatic activity of succinate dehydrogenase, malate dehydrogenase and ATPase were all inhibited by PBAF. We propose that PBAF is a potentially useful alternative for blue mold control and may act against P. italicum by interfering with respiration and disrupting the cell membrane.

Improvement of a gene targeting system for genetic manipulation in Penicillium digitatum

Penicillium digitatum is the most important pathogen of postharvest citrus. Gene targeting can be done in P. digitatum using homologous recombination via Agrobacterium tumefaciens mediated transformation (ATMT), but the frequencies are often very low. In the present study, we replaced the Ku80 homolog (a gene of the non-homologous end-joining (NHEJ) pathway) with the hygromycin resistance cassette (hph) by ATMT. No significant change in vegetative growth, conidiation, or pathogenicity was observed in Ku80-deficient strain (ΔPdKu80) of P. digitatum. However, using ΔPdKu80 as a targeting strain, the gene-targeting frequencies for both genes PdbrlA and PdmpkA were significantly increased. These results suggest that Ku80 plays an important role in homologous integration and the created ΔPdKu80 strain would be a good candidate for rapid gene function analysis in P. digitatum.

QoI Resistance in Fusicladium carpophilum Populations from Almond in California and Evaluation of Molecular Resistance Mechanisms

Disease management failures have been reported in California for almond scab caused by Fusicladium carpophilum following quinone outside inhibitor (QoI) applications. Resistance in the pathogen populations was found to be common and at high incidence in the major almond-growing regions beginning in 2003, 4 years after registration of azoxystrobin on this crop. Two levels of azoxystrobin resistance, moderate and high, were identified with 50% effective concentration (EC₅₀) values between 0.15 and 10 μg/ml or >40 μg/ml, respectively. Reference isolates collected before resistance was detected had EC₅₀ values <0.05 μg/ml. High-resistance was associated with a G143A mutation in the mitochondrial cytochrome b gene. For the less commonly found moderately resistant isolates, no mutations in the gene were detected between codons 122 and 212. Using primers targeting the G143A mutation or the cytochrome b gene of all F. carpophilum isolates in quantitative polymerase chain reaction (qPCR) analyses, the frequency of highly resistant isolates was accurately determined in mixtures of conidia with selected ratios of sensitive and resistant isolates. The frequency of high resistance in bulked samples of scab lesions, however, was generally underestimated compared with in vitro testing of fungicide sensitivity of fungal isolates from the same lesions. Competition experiments using conidial suspensions demonstrated stability of the highly resistant genotype in the presence of different amounts of sensitive and moderately resistant genotypes. Analysis of covariance of linear regressions of cycle threshold values on DNA concentrations derived from qPCR amplifications using two primer pairs for cytochrome b alleles with and without the G143 mutation showed that several isolates differed in their slopes and midpoints. Thus, heteroplasmy of mitochondrial-inherited QoI resistance is suggested as a likely cause for incongruence in estimating resistance frequencies using the two methods.

A novel green analytical procedure for monitoring of azoxystrobin in water samples by a flow injection chemiluminescence method with off-line ultrasonic treatment

A simple and green flow injection chemiluminescence (FI-CL) method for determination of the fungicide azoxystrobin was described for the first time. CL signal was generated when azoxystrobin was injected into a mixed stream of luminol and KMnO4 . The CL signal of azoxystrobin could be greatly improved when an off-line ultrasonic treatment was adopted. Meanwhile, the signal intensity increases with the analyte concentration proportionally. Several variables, such as the ultrasonic parameters, flow rate of reagents, concentrations of sodium hydroxide solution and CL reagents (potassium permanganate, luminol) were investigated, and the optimal CL conditions were obtained. Under optimal conditions, the linear range of 1-100 ng/mL for azoxystrobin was obtained and the detection limit (3σ) was determined as 0.13 ng/mL. The relative standard deviation was 1.5% for 10 consecutive measurements of 20 ng/mL azoxystrobin. The method has been applied to the determination of azoxystrobin residues in water samples.

Sensitivity of Monilinia fructicola from Brazil to Tebuconazole, Azoxystrobin, and Thiophanate-Methyl and Implications for Disease Management

The aim of this study was to investigate the sensitivity of Monilinia fructicola isolates to tebuconazole (demethylation inhibitor [DMI]), azoxystrobin (quinone outside inhibitor), and thiophanate-methyl (methyl benzimidazole carbamate) in 118 isolates collected from four states in Brazil from orchards with different histories of fungicide use. Sensitivity to fungicides was determined by inhibition of mycelial growth and spore germination on fungicide-amended media. Polymerase chain reaction was used to determine the frequencies of M. fructicola genotypes exhibiting high (HR) and low (LR) resistance to thiophanate-methyl among sampled populations. Resistance to tebuconazole was found in 15.8% of isolates collected from São Paulo State. The 50% effective concentration (EC₅₀) values varied from 0.01 to greater than 100 μg/ml. The EC₅₀ values for tebuconazole corresponded to its historic use frequency in the orchard; for instance, isolates from orchards with no DMI fungicide use had the lowest mean EC₅₀ value (0.04 μg/ml), while those collected from orchards where more than five DMI fungicide sprays were applied per season had a mean EC₅₀ value of 21.17 μg/ml. All isolates were sensitive to azoxystrobin but their EC₅₀, based on tests of inhibition of conidial germination, increased from 0.05 in 2002 to 0.44 μg/ml in 2008. The EC₅₀ values based on mycelial growth inhibition for thiophanate-methyl were >162 μg/ml, 1.99 to 12.5 μg/ml, and <1.0 μg/ml for HR, LR, and sensitive isolates, respectively.

Optimised expression and spectral analysis of the target enzyme CYP51 from Penicillium digitatum with possible new DMI fungicides

BACKGROUND

Sterol 14α-demethylase (CYP51), a key target of azole (DMI) fungicides, can be expressed in both prokaryotes and eukaryotes. Green mould of citrus, caused by Penicillium digitatum (Pers.) Sacc., is a serious post-harvest disease. To develop specific and more effective fungicides against this disease, the characteristics of the interaction between sterol 14α-demethylase from P. digitatum (PdCYP51) and possible new fungicides were analysed. The cyp51 gene of P. digitatum was cloned and expressed under different conditions in Escherichia coli (Mig.) Cast. & Chalm., and the binding spectra of PdCYP51 were explored by the addition of two commercial azoles and four new nitrogen compounds.

RESULTS

The yield of soluble protein (PdCYP51) was largest when expressed in Rosetta (DE3) induced by 0.5 mM IPTG for 8 h at 30 °C. Compound B (7-methoxy-2H-benzo[b][1,4]thiazine-3-amine) showed the strongest binding activity of the four new nitrogen compounds, with a K(d) value of 0.268 µM. The K(d) values of the six compounds were significantly correlated with their EC(50) values.

CONCLUSION

The spectral analysis and bioassay results could be used to screen the new chemical entities effectively. Compound B, selected by virtual screening from a commercial chemical library, is a candidate for a new DMI fungicide. These results provide a theoretical basis and new ideas for efficient design and development of new antifungal agents.

Determination of natural resistance frequencies in Penicillium digitatum using a new air-sampling method and characterization of fludioxonil- and pyrimethanil-resistant isolates

ABSTRACT Fungicide resistance was identified in natural populations of Penicillium digitatum, the causal agent of green mold of citrus, to two of three new postharvest fungicides before their commercial use. Using a new air-sampling method where large populations of the pathogen in citrus packinghouses were exposed to agar plates with a continuous, wide-range fungicide concentration gradient, isolates with reduced sensitivity to fludioxonil or pyrimethanil were obtained. Resistance frequencies to fludioxonil and pyrimethanil were calculated as 9.5 x 10(-7) to 1.5 x 10(-5) and 7.3 x 10(-6) to 6.2 x 10(-5), respectively. No isolates resistant to azoxystrobin were detected. Isolates with reduced sensitivity to fludioxonil or pyrimethanil were also obtained in laboratory selection studies, where high concentrations of conidial mixtures of isolates sensitive to the three fungicides were plated onto agar amended with each fungicide at 10 microg/ml. Isolates obtained from fludioxonil selection plates in laboratory and packinghouse experiments were placed into two categories based on mycelial growth: moderately resistant isolates had 50% effective concentration (EC(50)) values of 0.1 to 0.82 microg/ml and highly resistant isolates had EC(50) values > 1.5 microg/ml. Isolates resistant to pyrimethanil all had EC(50) values >8 microg/ml. Representative isolates of the two categories with reduced sensitivity to fludioxonil varied widely in their virulence and sporulation capacity as measured by the incidence of decay and degree of sporulation on inoculated fruit, respectively, whereas pyrimethanil-resistant isolates were mostly similar to the wild-type isolate. Fungicide sensitivity characteristics for isolates from fludioxonil and pyrimethanil selection plates remained stable after passages on nonamended agar, and disease could not be controlled after treatment with the respective fungicides. Types of fungicide resistance were visualized on thiabendazole- (TBZ) and imazalil-amended selection plates that were exposed in packinghouses where resistance to these fungicides was known to occur. The qualitative, single-site resistance to the benzimidazole TBZ was visualized by two distinct subpopulations in regard to fungicide sensitivity, whereas the quantitative, multi-site resistance to the demethylation inhibitor imazalil was apparent as a continuous density gradient of colonies along the fungicide concentration gradient. Types of resistance could not be assigned to fludioxonil or pyrimethanil because a limited number of resistant colonies was obtained on each plate. Thus, with this new method, we were able to estimate fungicide resistance frequencies as well as characterize and visualize types of resistance within populations of a fungal species. This information will be used to design resistance management strategies for previous and newly registered postharvest fungicides of citrus.