Quantification of conidial density of Aspergillus flavus and A. parasiticus in soil from almond orchards using real-time PCR

Botrytis fruit rot management: What have we achieved so far?

Botrytis cinerea is a destructive necrotrophic phytopathogen causing overwhelming diseases in more than 1400 plant species, especially fruit crops, resulting in significant economic losses worldwide. The pathogen causes rotting of fruits at both pre-harvest and postharvest stages. Aside from causing gray mold of the mature fruits, the fungus infects leaves, flowers, and seeds, which makes it a notorious phytopathogen. Worldwide, in the majority of fruit crops, B. cinerea causes gray mold. In order to effectively control this pathogen, extensive research has been conducted due to its wide host range and the huge economic losses it causes. It is advantageous to explore detection and diagnosis techniques of B. cinerea to provide the fundamental basis for mitigation strategies. Botrytis cinerea has been identified and quantified in fruit/plant samples at pre- and post-infection levels using various detection techniques including DNA markers, volatile organic compounds, qPCR, chip-digital PCR, and PCR-based nucleic acid sensors. In addition, cultural, physical, chemical, biological, and botanical methods have all been used to combat Botrytis fruit rot. This review discusses research progress made on estimating economic losses, detection and diagnosis, as well as management strategies, including cultural, physical, chemical, and biological studies on B. cinerea along with knowledge gaps and potential areas for future research.

Phyllosphere microbiome induces host metabolic defence against rice false-smut disease

Mutualistic interactions between host plants and their microbiota have the potential to provide disease resistance. Most research has focused on the rhizosphere, but it is unclear how the microbiome associated with the aerial surface of plants protects against infection. Here we identify a metabolic defence underlying the mutualistic interaction between the panicle and the resident microbiota in rice to defend against a globally prevalent phytopathogen, Ustilaginoidea virens, which causes false-smut disease. Analysis of the 16S ribosomal RNA gene and internal transcribed spacer sequencing data identified keystone microbial taxa enriched in the disease-suppressive panicle, in particular Lactobacillus spp. and Aspergillus spp. Integration of these data with primary metabolism profiling, host genome editing and microbial isolate transplantation experiments revealed that plants with these taxa could resist U. virens infection in a host branched-chain amino acid (BCAA)-dependent manner. Leucine, a predominant BCAA, suppressed U. virens pathogenicity by inducing apoptosis-like cell death through H2O2 overproduction. Additionally, preliminary field experiments showed that leucine could be used in combination with chemical fungicides with a 50% reduction in dose but similar efficacy to higher fungicide concentrations. These findings may facilitate protection of crops from panicle diseases prevalent at a global scale.

Quantification of the Aflatoxin Biocontrol Strain Aspergillus flavus AF36 in Soil and in Nuts and Leaves of Pistachio by Real-Time PCR

The species Aspergillus flavus and A. parasiticus are commonly found in the soils of nut-growing areas in California. Several isolates can produce aflatoxins that occasionally contaminate nut kernels, conditioning their sale. Strain AF36 of A. flavus, which does not produce aflatoxins, is registered as a biocontrol agent for use in almond, pistachio, and fig crops in California. After application in orchards, AF36 displaces aflatoxin-producing Aspergillus spp. and thus reduces aflatoxin contamination. Vegetative compatibility assays (VCAs) have traditionally been used to track AF36 in soils and crops where it has been applied. However, VCAs are labor intensive and time consuming. Here, we developed a quantitative real-time PCR (qPCR) protocol to quantify proportions of AF36 accurately and efficiently in different substrates. Specific primers to target AF36 and toxigenic strains of A. flavus and A. parasiticus were designed based on the sequence of aflC, a gene essential for aflatoxin biosynthesis. Standard curves were generated to calculate proportions of AF36 based on threshold cycle values. Verification assays using pure DNA and conidial suspension mixtures demonstrated a significant relationship by regression analysis between known and qPCR-measured AF36 proportions in DNA (R² = 0.974; P < 0.001) and conidia mixtures (R² = 0.950; P < 0.001). Tests conducted by qPCR in pistachio leaves, nuts, and soil samples demonstrated the usefulness of the qPCR method to precisely quantify proportions of AF36 in diverse substrates, ensuring important time and cost savings. The outputs of this study will serve to design better aflatoxin management strategies for pistachio and other crops.

Development of PCR, LAMP and qPCR Assays for the Detection of Aflatoxigenic Strains of Aspergillus flavus and A. parasiticus in Hazelnut

Aspergillus flavus and A. parasiticus are two species able to produce aflatoxins in foodstuffs, and in particular in hazelnuts, at harvest and during postharvest phase. As not all the strains of these species are aflatoxin producers, it is necessary to develop techniques that can detect aflatoxigenic from not aflatoxigenic strains. Two assays, a LAMP (loop-mediated isothermal amplification) and a real time PCR with TaqMan^® probe were designed and validated in terms of specificity, sensitivity, reproducibility, and repeatability. The capability of the strains to produce aflatoxins was measured in vitro and both assays showed to be specific for the aflatoxigenic strains of A. flavus and A. parasiticus. The limit of detection of the LAMP assay was 100–999 picograms of DNA, while the qPCR detected 160 femtograms of DNA in hazelnuts. Both techniques were validated using artificially inoculated hazelnuts and naturally infected hazelnuts. The qPCR was able to detect as few as eight cells of aflatoxigenic Aspergillus in naturally infected hazelnut. The combination of the LAMP assay, which can be performed in less than an hour, as screening method, with the high sensitivity of the qPCR, as confirmation assay, is able to detect aflatoxigenic strains already in field, helping to preserve the food safety of hazelnuts.

Quantitative detection of economically important Fusarium oxysporum f. sp. cubense strains in Africa in plants, soil and water

Banana is an important food crop and source of income in Africa. Sustainable production of banana, however, is at risk because of pests and diseases such as Fusarium wilt, caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). Foc can be disseminated from infested to disease-free fields in plant material, water and soil. Early detection of Foc using DNA technologies is thus required to accurately identify the fungus and prevent its further dissemination with plants, soil and water. In this study, quantitative (q)PCR assays were developed for the detection of Foc Lineage VI strains found in central and eastern Africa (Foc races 1 and 2), Foc TR4 (vegetative compatibility groups (VCG) 01213/16) that is present in Mozambique, and Foc STR4 (VCG 0120/15) that occurs in South Africa. A collection of 127 fungal isolates were selected for specificity testing, including endophytic Fusarium isolates from banana pseudostems, non-pathogenic F. oxysporum strains and Foc isolates representing the 24 VCGs in Foc. Primer sets that proved to be specific to Foc Lineage VI, Foc TR4 and Foc STR4 were used to produce standard curves for absolute quantification, and the qPCR assays were evaluated based on the quality of standard curves, repeatability and reproducibility, and limits of quantification (LOQ) and detection (LOD). The qPCR assays for Foc Lineage VI, TR4 and STR4 were repeatable and reproducible, with LOQ values of 10⁻³–10⁻⁴ ng/μL and a LOD of 10⁻⁴–10⁻⁵ ng/μL. The quantitative detection of Foc strains in Africa could reduce the time and improve the accuracy for identifying the Fusarium wilt pathogen from plants, water and soil on the continent.

Inoculum quantification of canker-causing pathogens in prune and walnut orchards using real-time PCR

AIMS

A real-time quantitative PCR (qPCR) assay was established to quantify the inoculum densities in the air and rainwater for six canker-causing pathogen groups in prune and walnut orchards in California.

METHODS AND RESULTS

The previously published DNA primers to target six pathogen groups including Botryosphaeria dothidea, Cytospora spp., Diplodia spp., Lasiodiplodia spp., Neofusicoccum spp. and Phomopsis spp. were used in a qPCR assay. Air samples from Burkard spore traps and rain samples from special rain collector devices were collected periodically from various prune and walnut orchards. Using the qPCR approach, we were able to quantify the concentrations of these pathogen groups in rainwater and air samples and study the dynamics of pathogen inoculum in orchards showing severe canker potential. Phomopsis spp. and Diplodia spp. were not found in all rain samples in prune orchards, although they were detected in the 2016 in the walnut orchard. The other four pathogen groups were quantified at varying concentrations in the prune and walnut orchards. Cytospora spp. in some cases showed higher concentrations in the rainwater in prune orchards.

CONCLUSIONS

The rainy season during winter and early spring is a highly risky period of time for infection by the pathogens when the inoculum of these pathogens can easily spread by air and rain water, thus serving as an important inoculum source for disease initiation. The different studied pathogen groups showed different concentrations during the growing season, indicating the complexity of the components of canker-causing species in various tree crops.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study showed the applicability of the qPCR assay in the quantification of inoculum in tree orchards to help reveal the mechanisms of canker disease epidemics and to help design disease management strategies.

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.

Development and Application of a Quantitative PCR Detection Method to Quantify Venturia oleaginea in Asymptomatic Olive (Olea europaea) Leaves

Olive leaf spot (OLS), caused by Venturia oleaginea, is one of the most common and serious diseases of olive trees in the Mediterranean region. Understanding the pathogen life cycle is important for the development of effective control strategies. Current knowledge is incomplete owing to a lack of effective detection methods. It is extremely difficult to culture V. oleaginea in vitro, so primers were designed to amplify and sequence the internal transcribed spacer ITS1-5.8S-ITS2 region of the fungus directly from infected olive leaves. Sanger sequencing indicated a unique ITS region present in the European strains screened, confirming the appropriateness of the target region for developing a quantitative PCR (qPCR) assay. Furthermore, high-throughput sequencing of the same region excluded the presence of other Venturia species in the olive phyllosphere. The qPCR assay proved very specific and sensitive, enabling the detection of approximately 26 copies of target DNA. The analysis of symptomless leaves during early stages of the epidemic from the end of winter through spring revealed a similar quantity of pathogen DNA regardless of the leaf growth stage. In contrast, the pathogen titer changed significantly during the season. Data indicated that leaf infections start earlier than expected over the season and very young leaves are as susceptible as adult leaves. These findings have important practical implications and suggest the need for improved scheduling of fungicide treatments. The qPCR assay represents a valuable tool providing quantitative results and enables detection of V. oleaginea in all olive organs, including those in which OLS cannot be studied using previously available methods.

Improved Evaluation of Wheat Cultivars (Lines) on Resistance to Puccinia striiformis f. sp. tritici Using Molecular Disease Index

Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is one of the most destructive diseases of wheat worldwide. Sichuan Province plays an important role in interregional epidemics in China. Application of host resistance is important in disease management, and efficient approaches to evaluate resistance level are necessary to obtain useful varieties. In this study, 100 wheat cultivars (lines) growing in Sichuan were selected to evaluate their resistance to stripe rust. Field experiments were conducted with a mixture of three P. striiformis f. sp. tritici races for inoculations at seeding and adult stages in the 2014 to 2015 season and the 2016 to 2017 season. Leaf samplings were conducted four times during the latent period at early growth stage of wheat. The sampled leaves were processed to extract DNA. The DNA of both wheat and P. striiformis f. sp. tritici was quantified using real-time quantitative polymerase chain reaction, and the molecular disease index (MDI) was used to evaluate the resistance level. The area under the disease progress curve in terms of disease index (AUDPC-DI) was obtained for each studied cultivar (line) in the fields. Among the 100 studied cultivars (lines), 61% of them showed seedling resistance, and 63 and 65% showed adult resistance in the 2014 to 2015 and 2016 to 2017 seasons, respectively, based on the infection type. High consistency in resistance grouping by cluster analysis as the percentage of the studied cultivar (line) belonging to the same group based on AUDPC-DI data and based on MDI data was obtained. The correlations between AUDPC-DI and MDI from samples collected on 9 and 14 or 15 days after inoculation during the latent period were all significant at P < 0.01. This study provided a new and efficient method for evaluation of varietal resistance to wheat stripe rust.

Accelerated Development and Toxin Tolerance of the Navel Orangeworm Amyelois transitella (Lepidoptera: Pyralidae) in the Presence of Aspergillus flavus

The navel orangeworm (Amyelois transitella) and the fungus Aspergillus flavus constitute a facultative mutualism and pest complex in tree nut and fruit orchards in California. The possibility exists that the broad detoxification capabilities of A. flavus benefit its insect associate by metabolizing toxicants, including hostplant phytochemicals and pesticides. We examined this hypothesis by conducting laboratory bioassays to assess growth rates and survivorship of pyrethroid-resistant (R347) and susceptible (CPQ) larval strains on potato dextrose agar diet containing almond meal with and without two furanocoumarins, xanthotoxin and bergapten, found in several hostplants, and with and without two insecticides, bifenthrin and spinetoram, used in almond and pistachio orchards. Additionally, fungi were incubated in liquid diets containing the test chemicals, and extracts of these diets were added to almond potato dextrose agar (PDA) diets and fed to larvae to evaluate the ability of the fungus to metabolize these chemicals. Larvae consuming furanocoumarin-containing diet experienced higher mortality than individuals on unamended diets, but adding A. flavus resulted in up to 61.7% greater survival. Aspergillus flavus in the diet increased development rate > two-fold when furanocoumarins were present, demonstrating fungal enhancement of diet quality. Adding extracts of liquid diets containing xanthotoxin and fungus decreased mortality compared to xanthotoxin alone. On diets containing bifenthrin and spinetoram, however, mortality increased. These results support the hypothesis that A. flavus enhances navel orangeworm performance and contributes to detoxification of xenobiotics. Among practical implications of our findings, this mutualistic association should be considered in designing chemical management strategies for these pests.

Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR

Identification of populations of Aspergillus section Nigri species in environmental samples using traditional methods is laborious and impractical for large numbers of samples. We developed species-specific primers and probes for quantitative droplet digital PCR (ddPCR) to improve sample throughput and simultaneously detect multiple species in each sample. The ddPCR method was used to distinguish Aspergillus niger, Aspergillus welwitschiae, Aspergillus tubingensis and Aspergillus carbonarius in mixed samples of total DNA. Relative abundance of each species measured by ddPCR agreed with input ratios of template DNAs. Soil samples were collected at six time points over two growing seasons from two raisin vineyards in Fresno County, California. Aspergillus section Nigri strains were detected in these soils in the range of 10² -10⁵  CFU g^-1 . Relative abundance of each species varied widely among samples, but in 52 of 60 samples, A. niger was the most abundant species, ranging from 38 to 88% of the total population. In combination with total plate counts, this ddPCR method provides a high-throughput method for describing population dynamics of important potential mycotoxin-producing species in environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to demonstrate the utility of ddPCR as a means to quantify species of Aspergillus section Nigri in soil. This method eliminates the need for isolation and sequence identification of individual fungal isolates, and allows for greater throughput in measuring relative population sizes of important (i.e. mycotoxigenic) Aspergillus species within a population of morphologically indistinguishable species.

Larval Preference and Performance of Amyelois transitella (Navel Orangeworm, Lepidoptera: Pyralidae) in Relation to the Fungus Aspergillus flavus

The navel orangeworm, Amyelois transitella (Walker), is a polyphagous pest of California nut crops and is responsible for extensive losses in the United States. It directly damages crops by feeding and contaminating nuts with frass and webbing and vectors saprophytic fungi that infect crops. The navel orangeworm is commonly associated with Aspergillus species, including the toxigenic Aspergillus flavus, which causes crop loss by producing carcinogens, including aflatoxin B1. This lepidopteran-fungus association is the most economically serious pest complex in Central Valley orchards, and evidence indicates that this relationship is mutualistic. We assessed preference and performance of navel orangeworm larvae associated with A. flavus in behavioral bioassays in which neonates were allowed to orient within arenas to media with or without fungal tissue, and performance bioassays in which larvae were reared with and without A. flavus on potato dextrose agar (PDA) and a semidefined almond PDA diet to evaluate effects on development and pupal weight. Navel orangeworm larvae were attracted to A. flavus and developed faster in its presence, indicating a nutritional benefit to the caterpillars. Larvae reached pupation ∼33% faster on diet containing A. flavus, and pupal weights were ∼18% higher for males and ∼13% higher for females on this diet. Our findings indicate that A. flavus plays an important role in larval orientation and development on infected hosts. The preference-performance relationship between navel orangeworms and Aspergillus flavus is consistent with a facultative mutualism that has broad implications for pest management efforts and basic understanding of Lepidoptera-plant interactions.

Natural phenolic metabolites from endophytic Aspergillus sp. IFB-YXS with antimicrobial activity

Prompted by the pressing necessity to conquer phytopathogenic infections, the antimicrobial compounds were characterized with bioassay-guided method from the ethanol extract derived from the solid-substrate fermentation of Aspergillus sp. IFB-YXS, an endophytic fungus residing in the apparently healthy leave of Ginkgo biloba L. The aim of this work was to evaluate the antimicrobial activity and mechanism(s) of these bioactive compounds against phytopathogens. Among the compounds, xanthoascin (1) is significantly inhibitory on the growth of the phytopathogenic bacterium Clavibacter michiganense subsp. Sepedonicus with a minimum inhibitory concentration (MIC) value of 0.31μg/ml, which is more potent than streptomycin (MIC 0.62μg/ml), an antimicrobial drug co-assayed herein as a positive reference. Moreover, terphenyl derivatives 3, 5 and 6 are also found to be active against other phytopathogens including Xanthomonas oryzae pv. oryzae Swings, Xanthomonas oryzae pv. oryzicola Swings, Erwinia amylovora and Pseudomonas syringae pv. lachrymans etc. The antibacterial mechanism of xanthoascin (1) was addressed to change the cellular permeability of the phytopathogens, leading to the remarkable leakage of nucleic acids out of the cytomembrane. The work highlights the possibility that xanthoascin (1), an analogue of xanthocillin which is used to be an approved antibiotic, may find its renewed application as a potent antibacterial agrichemical. This study contributes to the development of new antimicrobial drugs, especially against C. michiganense subsp. Sepedonicus.

Detection of Aspergillus flavus in stored peanuts using real-time PCR and the expression of aflatoxin genes in toxigenic and atoxigenic A. flavus isolates

Aspergillus flavus is the main species from section Flavi responsible for aflatoxin accumulation in stored peanuts. Rapid methods to detect A. flavus could help to prevent aflatoxins from entering the food chain. A real-time polymerase chain reaction (RTi-PCR) assay was standardized for rapid, specific, and sensitive detection of A. flavus in stored peanuts. A. flavus was detected in 53.6% and 50% of peanut samples by RTi-PCR and A. flavus and Aspergillus parasiticus agar culture, respectively, with 95% agreement between them. Twenty-two A. flavus isolates were screened using high-performance liquid chromatography for their capacity to produce aflatoxin AFB1 (B1). B1 was produced by >72% of the isolates. Sixteen isolates produced B1 at concentrations ranging from 1.64 to 109.18 μg/mL. Four aflatoxin biosynthetic pathway genes (aflD, aflM, aflP, and aflQ) were evaluated using PCR and reverse-transcription PCR in 22 A. flavus isolates from peanut kernels with the aim of rapidly and accurately differentiating toxigenic and atoxigenic isolates. The PCR amplification of genes did not correlate with aflatoxin production capability. The expression of aflD and aflQ was a good marker for differentiating toxigenic from atoxigenic isolates.

The use of real-time PCR to study Penicillium chrysogenum growth kinetics on solid food at different water activities

Fungal growth on solid foods can make them unfit for human consumption, but certain specialty foods require fungi to produce their characteristic properties. In either case, a reliable way of measuring biomass is needed to study how various factors (e.g. water activity) affect fungal growth rates on these substrates. Biochemical markers such as chitin, glucosamine or ergosterol have been used to estimate fungal growth, but they cannot distinguish between individual species in mixed culture. In this study, a real-time polymerase chain reaction (rt-PCR) protocol specific for a target fungal species was used to quantify its DNA while growing on solid food. The measured amount of DNA was then related to the biomass present using an experimentally determined DNA-to-biomass ratio. The highly sensitive rt-PCR biomass assay was found to have a wide range, able to quantify the target DNA within a six orders-of-magnitude difference. The method was used to monitor germination and growth of Penicillium chrysogenum spores on a model porous food (cooked wheat flour) at 25°C and different water activities of 0.973, 0.936, and 0.843. No growth was observed at 0.843, but lag, exponential and stationary phases were identified in the growth curves for the higher water activities. The calculated specific growth rates (μ) during the exponential phase were almost identical, at 0.075/h and 0.076/h for aw=0.973 and 0.936, respectively. The specificity of the method was demonstrated by measuring the biomass of P. chrysogenum while growing together with Aspergillus niger on solid media at aw=0.973.

Modulation of antimicrobial metabolites production by the fungus Aspergillus parasiticus

Biosynthesis of active secondary metabolites by fungi occurs as a specific response to the different growing environments. Changes in this environment alter the chemical and biological profiles leading to metabolites diversification and consequently to novel pharmacological applications. In this work, it was studied the influence of three parameters (fermentation length, medium composition and aeration) in the biosyntheses of antimicrobial metabolites by the fungus Aspergillus parasiticus in 10 distinct fermentation periods. Metabolism modulation in two culturing media, CYA and YES was evaluated by a 2(2) full factorial planning (ANOVA) and on a 2(3) factorial planning, role of aeration, medium composition and carbohydrate concentration were also evaluated. In overall, 120 different extracts were prepared, their HPLC profiles were obtained and the antimicrobial activity against A. flavus, C. albicans, E. coli and S. aureus of all extracts was evaluated by microdilution bioassay. Yield of kojic acid, a fine chemical produced by the fungus A. parasiticus was determined in all extracts. Statistical analyses pointed thirteen conditions able to modulate the production of bioactive metabolites by A. parasiticus. Effect of carbon source in metabolites diversification was significant as shown by the changes in the HPLC profiles of the extracts. Most of the extracts presented inhibition rates higher than that of kojic acid as for the extract obtained after 6 days of fermentation in YES medium under stirring. Kojic acid was not the only metabolite responsible for the activity since some highly active extracts showed to possess low amounts of this compound, as determined by HPLC.

Field Distribution of Wheat Stripe Rust Latent Infection Using Real-Time PCR

Stripe rust of wheat, caused by Puccinia striiformis f. tritici, is of worldwide significance. Quantification of latent infection level is critical to estimate the potential for disease epidemics. In this study, field distribution of latent infection and the corresponding observed disease were studied in two growing seasons from 2009 to 2011 in Gangu, Gansu Province and Shangzhuang, Beijing, China. A previously developed real-time polymerase chain reaction (PCR) assay was applied to obtain the molecular disease index (MDX) to quantify the level of latent infection. At 1 to 3 weeks after leaf sampling, the observed disease indices (DX) were assessed in the corresponding experimental sites. The computer software SURFER showed that the spatial distribution patterns of MDX had a linear relationship with DX in field plots with P = 0.01. The aggregation levels of MDX correlated with those of DX in the fields. The disease foci which were correctly detected for latent infections with the real-time PCR for the Gangu and Shangzhuang field plots were 71.4 and 85.7%, respectively. The triadimefon fungicide treatment focused on the detected latent infection foci reduced both the initial inoculum and disease development, resulting in an average reduction in disease area in the field plots of 73 to 81%.

A New TaqMan Real-Time Polymerase Chain Reaction Assay for Quantification of Fusarium virguliforme in Soil

The quantification of the soilborne pathogen Fusarium virguliforme inoculum in soil is important for epidemiological studies of soybean sudden death syndrome (SDS). Classical dilution plating methods to determine inoculum density in soil have yielded inconsistent results due to slow growth, variable colony morphology of the pathogen, and the presence of other fungi with similar phenotype. A TaqMan real-time polymerase chain reaction assay was developed based on sequences of the FvTox1 gene of F. virguliforme. The gene differed by four single-nucleotide proteins from the other SDS-causing species. Assay specificity was tested on 48 fungal isolates that varied in taxonomic relatedness. Assay sensitivity was appraised on 10-fold serial dilutions of genomic DNA, conidia suspensions, and soil spiked with conidia. Applicability of the assay was evaluated on field and greenhouse soil samples, and on roots of symptomatic plants. The assay detected only DNA sequences specific to F. virguliforme. The detection limit of the assay was 5 pg/μl, 1,000 conidia/ml, and 1,000 conidia/g soil for genomic DNA, conidial suspensions, and soil with conidia, respectively. The assay was specific to F. virguliforme and was used successfully to quantify inoculum density in soil and soybean roots. The assay can be used as a diagnostic tool for rapid screens of field and greenhouse soil, and for symptomatic and asymptomatic plants.