A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f. sp. cucumerinum and f. sp. radicis‐cucumerinum

Lievens, Bart; Claes, Loes; Vakalounakis, D. J.; Vanachter, A.; Thomma, B.P.H.J.

doi:10.1111/j.1462-2920.2007.01329.x

Cited by 94 publications

(50 citation statements)

References 59 publications

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“…The sequence was truncated when bases lower than Q20 were detected, and the final sequence length was restricted to >150 bp (sequences with ambiguous base calls (N) were excluded). Secondly, sequences were connected with FLASH software (Lievens et al 2007) using an overlap of >10 bp between reads 1 and 2, and base mismatches were not allowed. Lastly, the effective sequence of each sample (with fully matched indices) was extracted based on the sequence information used to distinguish the samples.…”

Section: Soil Microbial Propertiesmentioning

confidence: 99%

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Zhao

Zhang

et al. 2017

J Soils Sediments

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Purpose We examined the effects of vermicompost application as a basal fertilizer on the properties of a sandy loam soil used for growing cucumbers under continuous cropping conditions when compared to inorganic or organic fertilizers. Materials and methods A commercial cucumber (Cucumis sativus L.) variety was grown on sandy loam soil under four soil amendment conditions: inorganic compound fertilizer (750 kg/ha,), replacement of 150 kg/ha of inorganic compound fertilizer with 3000 kg/ha of organic fertilizer or vermicompost, and untreated control. Experiments were conducted in a greenhouse for 4 years, and continuous planting resulted in seven cucumber crops. The yield and quality of cucumber fruits, basic physical and chemical properties of soil, soil nutrient characteristics, and the soil fungal community structure were measured and evaluated. Results and discussion Continuous cucumber cropping decreased soil pH and increased electrical conductivity. However, application of vermicompost significantly improved several soil characteristics and induced a significant change in the rhizosphere soil fungal community compared to the other treatments. Notably, the vermicompost amendments resulted in an increase in the relative abundance of Ascomycota, Chytridiomycota, Sordariomycetes, Eurotiomycetes, and Saccharomycetes, and a decrease in Glomeromycota, Zygomycota, Dothideomycetes, Agaricomycetes, and Incertae sedis. Compared to the organic fertilizer treatment, vermicompost amendment increased the relative abundance of beneficial fungi and decreased those of pathogenic fungi. Cucumber fruit yield decreased yearly under continuous cropping conditions, but both inorganic and organic fertilizer amendments increased yields. Vermicompost amendment maintained higher fruit yield and quality under continuous cropping conditions. Conclusions Continuous cropping decreased cucumber yield in a greenhouse, but basic fertilizer amendment reduced this decline. Moreover, basal fertilizer amendment decreased beneficial and pathogenic fungi, and the use of vermicompost amendment in the basic fertilizer had a positive effect on the health of the soil fungal community.

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Section: Soil Microbial Propertiesmentioning

confidence: 99%

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Zhao

Zhang

et al. 2017

J Soils Sediments

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“…radicis-cucumerinum (FORC), causing Fusarium root and stem rot (Vakalounakis 1996). Both pathogens are morphologically identical, with the same host range, but expressing slightly different disease symptoms (Lievens et al 2007;Vakalounakis 1996). Fusarium root and stem rot can be seen in most cucumber growing regions around the world (Neshev 2008;Lauenstein 1955;Martyn 1996;Jenkins & Wehner 1983).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Resistance, Enzymatic Response, and Phenolic Compounds in Roots of F₁Cucumber Hybrids to Fusarium Oxysporum F. Sp. Radicis-Cucumerinum

Moghbeli

Nemati

Aroiee

et al. 2017

Journal of Horticultural Research

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Cucumber (Cucumis sativus L.) is widely cultivated in many parts of the world. Its production is significantly affected by Fusarium root and stem rot, which is caused by the fungus Fusarium oxysporum f. sp. radicis-cucumerinum, a major disease of cucumber in some regions. Most of the management programs for the control of Fusarium root and stem rot are not successful; therefore, growing resistant cultivars may be the best solution. Use of disease-resistant cultivars is a key to environmentally friendly and economically sustainable disease control in modern crop production. To find resistance sources, 10 F1 cucumber hybrids were screened against F. oxysporum f. sp. radicis-cucumerinum. Total phenolic content (PC), soluble peroxidase (POX), and polyphenol oxidase (PPO) activities were evaluated at 0, 4, and 8 days after inoculation. Significant differences were observed between resistant and susceptible genotypes in increase of total PCs and enzymatic activities at fourth day after inoculation. These findings can be used in breeding programs of cucumber aiming at creating F1 cultivars resistant to Fusarium root and stem rot.

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“…The data generated with the LD assay were compared with data obtained by TaqMan PCR detection for a selected range of targets for which TaqMan probes were available (Phytophthora spp., P. aphanidermatum, and V. dahliae) and data obtained by SYBR green-based PCR detection for F. oxysporum spp. (35).…”

Section: Resultsmentioning

confidence: 99%

Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay

Doorn

Slawiak

Szemes

et al. 2009

Appl Environ Microbiol

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Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, backgroundfree ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5 and 3 ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10 4 . A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.

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A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f. sp. cucumerinum and f. sp. radicis‐cucumerinum

Cited by 94 publications

References 59 publications

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Evaluation of Resistance, Enzymatic Response, and Phenolic Compounds in Roots of F₁Cucumber Hybrids to Fusarium Oxysporum F. Sp. Radicis-Cucumerinum

Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay

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A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f. sp. cucumerinum and f. sp. radicis‐cucumerinum

Cited by 94 publications

References 59 publications

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Effects of vermicompost amendment as a basal fertilizer on soil properties and cucumber yield and quality under continuous cropping conditions in a greenhouse

Evaluation of Resistance, Enzymatic Response, and Phenolic Compounds in Roots of F1Cucumber Hybrids to Fusarium Oxysporum F. Sp. Radicis-Cucumerinum

Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay

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Evaluation of Resistance, Enzymatic Response, and Phenolic Compounds in Roots of F₁Cucumber Hybrids to Fusarium Oxysporum F. Sp. Radicis-Cucumerinum