Real-time PCR quantification of Fusarium avenaceum in soil and seeds

A rapid real-time PCR assay for detecting Microdochium paspali causing sparse leaf patch on seashore paspalum and in environmental samples

BACKGROUND

Sparse leaf patch (SLP) is one of the most significant diseases affecting seashore paspalum (Paspalum vaginatum Sw.), caused by Microdochium paspali. Fast and accurate detection of this pathogen is crucial for effective disease management. However, conventional culture-based methods are time-consuming and often compromised by the presence of other saprophytic or endophytic fungi.

RESULTS

In this study, we developed a real-time fluorescent quantitative (q)PCR method based on the internal transcribed spacer (ITS) region of the ribosomal RNA gene to rapidly detect and quantify M. paspali. The qPCR assay demonstrated the ability to detect all 12 tested isolates of M. paspali, with no cross-reactions observed when tested against 30 isolates of other fungal pathogens from turfgrass samples. The detection limit of the qPCR method was as low as 3.65 × 102 copies μL-1 of M. paspali genomic DNA, and the entire detection process could be completed within 1 h. The fluorescence signal was detectable in the leaf tissues of seashore paspalum without apparent disease symptoms as early as 24 h postinoculation with M. paspali. Moreover, the qPCR method successfully detected M. paspali in both asymptomatic and symptomatic turfgrass samples, including leaf, stem, root and rhizosphere soil, indicating that this assay can significantly enhance the detection of M. paspali.

CONCLUSION

The study developed a rapid real-time qPCR assay for the detection of M. paspali causing SLP on seashore paspalum and in environmental samples, which has important implications for early warning and management of SLP. © 2024 Society of Chemical Industry.

Fusarium equiseti as an Emerging Foliar Pathogen of Lettuce in Greece: Identification and Development of a Real-Time PCR for Quantification of Inoculum in Soil Samples

Lettuce is the most commonly cultivated leafy vegetable in Greece, available in the market throughout the year. In this study, an emerging foliar disease observed in commercial farms has been associated to the pathogen Fusarium equiseti, a member of the Fusarium incarnatum-equiseti species complex (FIESC). Thirty F. equiseti isolates obtained from symptomatic lettuce plants were identified on the basis of morphology and evaluated for their pathogenicity. The isolates were further characterized using amplification and sequence analysis of the internal transcribed region (ITS-rDNA), and of the translation elongation factor 1-alpha (TEF1-a), calmodulin (CAM), beta-tubulin (Bt), and small subunit (SSU) genes. Moreover, a novel RT-qPCR assay was developed, designing a primer pair and a probe based on the TEF1-a sequences. This assay showed high specificity, amplifying F. equiseti DNA samples, while no amplification product was observed from samples of other common soilborne fungi. The generated RT-qPCR assay could be a useful tool for the detection and quantification of F. equiseti in soil samples deriving from fields cultivated with lettuce and other leafy vegetables, hosts of this specific pathogen.

A Quantitative PCR Assay for Detection and Quantification of Fusarium sambucinum

Fusarium sambucinum is an ascomycete that has been isolated from a broad range of plant hosts, including hop (Humulus lupulus L.), where it acts as a causal agent of Fusarium canker, a disease that can impact cone quality and yield in severe cases. Current diagnostic methods rely on isolation of the fungus from plant tissue, a time- and resource-intensive process with limited sensitivity, complicated by the potential presence of other Fusarium spp. that have been reported on hop. Our objective was to develop a rapid and sensitive diagnostic tool to detect and quantify F. sambucinum in plant tissues. Using a modified random amplified polymorphic DNA PCR assay, we identified a F. sambucinum-specific marker that serves as the target in a TaqMan (hydrolysis) probe quantitative PCR (qPCR) assay that can be used to detect F. sambucinum DNA in a background of plant DNA. When used to screen 52 isolates of F. sambucinum and isolates representing 13 other Fusarium spp., the assay was robust in detecting F. sambucinum while discriminating between F. sambucinum and closely related Fusarium spp., including F. venenatum. Furthermore, this assay reliably detects as little as 1 pg of F. sambucinum DNA in a background of total DNA from plant tissue. Within-sample comparisons of this qPCR assay with traditional cultural isolation methods demonstrated the greater sensitivity of the qPCR-based method for detection of F. sambucinum. When used to screen 220 asymptomatic stem samples, the qPCR assay detected F. sambucinum in 100 samples (45.5%); by comparison, F. sambucinum was detected in only 3 samples (1.4%) by culturing methods. Moreover, quantification of F. sambucinum DNA was possible for 60 of these samples, indicating the utility of the qPCR assay for early detection. This assay should be useful in diagnostic and epidemiological applications to detect and quantify F. sambucinum from multiple hosts and environmental samples.

Prevalence of Fusarium fungi and Deoxynivalenol Levels in Winter Wheat Grain in Different Climatic Regions of Poland

Fusarium head blight (FHB) caused by fungi of the genus Fusarium is one of the most dangerous crop diseases, which has a wide geographic distribution and causes severe economic losses in the production of major cereal species. The infection leads to the accumulation of mycotoxins in grains, which compromises its suitability for human and animal consumption. The study demonstrated that grain samples from warmer regions of Poland, including Sulejów and Tomaszów Bolesławicki (results differed across years of the study), were colonized mainly by F. graminearum and were most highly contaminated with deoxynivalenol (DON). Samples from Northeastern Poland, i.e., Ruska Wieś, which is located in a cooler region, were characterized by a predominance of Fusarium species typical of the cold climate, i.e., Fusarium poae and Penicillium verrucosum. A Spearman's rank correlation analysis revealed that the severity of grain infection with F. avenaceum/F. tricinctum was affected by the mean daily temperature and high humidity in May, and the corresponding values of the correlation coefficient were determined at R = 0.54 and R = 0.50. Competitive interactions were observed between the F. avenaceum/F. tricinctum genotype and DON-producing F. culmorum and F. graminearum, because the severity of grain infections caused by these pathogens was bound by a negative correlation.

Goldenrod Root Compounds Active against Crop Pathogenic Fungi

Root extracts of three goldenrods were screened for antimicrobial compounds. 2Z,8Z- and 2E,8Z-matricaria esters from European goldenrod (Solidago virgaurea) and E- and Z-dehydromatricaria esters from grass-leaved goldenrod (Solidago graminifolia) and first from showy goldenrod (Solidago speciosa) were identified by high-performance thin-layer chromatography combined with effect-directed analysis and high-resolution mass spectrometry or nuclear magnetic resonance spectroscopy after liquid chromatographic fractionation and isolation. Next to their antibacterial effects (against Bacillus subtilis, Aliivibrio fischeri, and Pseudomonas syringae pv. maculicola), they inhibited the crop pathogenic fungi Fusarium avenaceum and Bipolaris sorokiniana with half maximal inhibitory concentrations (IC₅₀) between 31 and 107 μg/mL. Benzyl 2-hydroxy-6-methoxybenzoate, for the first time found in showy goldenrod root, showed the strongest antifungal effect, with IC₅₀ of 25-26 μg/mL for both fungal strains.

Potential inoculum sources of Fusarium species involved in asparagus decline syndrome and evaluation of soil disinfestation methods by qPCR protocols

BACKGROUND

Asparagus decline syndrome (ADS), one of the most important diseases affecting asparagus crops, causes important yield losses worldwide. Fusarium proliferatum, F. oxysporum and F. redolens are among the main species associated with ADS. To explore their potential inoculum sources and the effectiveness of soil disinfestation practices for ADS management, molecular methods based on a quantitative real-time polymerase chain reaction (qPCR) were developed. qPCR-based molecular tools demonstrated advantages in the sensitive and specific detection and quantification of fungal pathogens in comparison with less-accurate and time-consuming traditional culture methods.

RESULTS

F. proliferatum, F. oxysporum and F. redolens could be specifically detected and accurately quantified in asparagus plants, soil and irrigation water collected from asparagus fields with ADS symptoms by means of the designed TaqMan qPCR protocols. Furthermore, these molecular tools were successfully applied for evaluation of the efficacy of diverse soil disinfestation treatments. Chemical fumigation with dazomet and biosolarization with pellets of Brassica carinata contributed to a significant reduction in the inoculum densities of the three Fusarium species in treated soils, which was correlated with production increases.

CONCLUSIONS

The capability to accurately detect and quantify the main Fusarium species involved in ADS in plants, soil and water samples by means of qPCR will allow identification of high-risk fields that can be avoided or managed to reduce yield losses. Quantification of pathogen densities in the soil may also provide essential insights into the effectiveness of soil disinfestation methods for ADS management. © 2021 Society of Chemical Industry.

Bioactive clerodane diterpenes of giant goldenrod (Solidago gigantea Ait.) root extract

Giant goldenrod (Solidago gigantea Ait.) root extract was screened for bioactive compounds by high-performance thin-layer chromatography (HPTLC), coupled with effect-directed analysis including antibacterial (Bacillus subtilis F1276, B. subtilis subsp. spizizenii, Aliivibrio fischeri and Xanthomonas euvesicatoria), antifungal (Fusarium avenaceum) and enzyme inhibition (acetyl- and butyrylcholinesterases, α- and β-glucosidases and α-amylase) assays. Compounds of six multipotent zones (Sg1-Sg6) were characterized by HPTLC-heated electrospray ionization-high-resolution mass spectrometry (HRMS) and HPTLC-Direct Analysis in Real Time-HRMS. Apart from zone Sg3, containing three compounds, a single characteristic compound was detectable in each bioactive zone. The bioassay-guided isolation using preparative-scale flash chromatography and high-performance liquid chromatography provided eight compounds that were identified by NMR spectroscopy as clerodane diterpenes. All isolates possessed inhibiting activity against at least one of the tested microorganisms.