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Povzetek: A list of general minimum criteria was developed to be used in preparation of reference materials to be used in interlaboratory testing, including validations through test performance studies. The list was based on previously identified criteria in standards including ISO standards, EPPO guidelines, deliverables of relevant projects, related fields, and own experience of project partners. Several additional criteria were proposed: ‘availability’, ‘purity’ and ‘commutability’. These criteria result from a series of discussions, taking into account previous work and relevant international standards. Where relevant, each criterion was first defined as a series of levels from the highest to lowest ranking with the lowest ranking considered to be the minimum. Depending on the intended use, the reference material may need to fulfil higher levels of selected criteria or some criteria may not be relevant at all. The criteria were tested by the organizers of the TPS in round 1 of validation within VALITEST project which include bacteria, viruses, nematodes and fungi. The systematic and structured approach of describing RMs was found to be useful in promoting transparent descriptions of the RMs used and comparability of TPSs, as well as a step toward implementing FAIR data principles. The criteria defined here are applicable, potentially with minor modification, beyond the scope of this deliverable and project to other pests and other uses of RMs
Ključne besede: pests, tests
Objavljeno v DiRROS: 03.09.2024; Ogledov: 113; Prenosov: 863
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Povzetek: The aim of the deliverable 1.4. is to present a summary of the results obtained in the Round 1 of the test performance studies (TPS) organized by WP1 on six prioritized pests. Tests selection for each TPS was conducted following the “Common rules for selection of tests for TPS” and based on the “Weighted criteria for selection of tests for TPS”, both described in deliverable D1.1, while the list of selected tests for each TPS is available and explained in deliverable D1.2. TPS participants were selected following the “Common rules for selection of participants for TPS” and based on the “Criteria for selection of participants of TPS”, also both described in deliverable D1.1. For each of the six TPSs, the methodology used to perform the tests, the results of preliminary studies to select the tests, the results of the TPS and their thorough analysis and interpretation are described in corresponding TPS reports (supplementary information available upon request under confidentiality agreement). The validation data obtained during the six TPSs will be available in the validation section of the EPPO database on the diagnostic expertise. Main outcomes for each of the TPSs are highlighted as well as difficulties noticed during the organization process, which will improve organization of the following studies in the Round 2.
Ključne besede: test performance study, plant diseases
Objavljeno v DiRROS: 03.09.2024; Ogledov: 147; Prenosov: 68
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Povzetek: Dickeya fangzhongdai, an aggressive plant pathogen, causes symptoms on a variety of crops and ornamental plants including bleeding canker of Asian pear trees. Historical findings stress the need for a specific detection tool for D. fangzhongdai to prevent overlooking the pathogen or assigning it to general Dickeya spp. Therefore, a qualitative real-time PCR for specific detection of D. fangzhongdai has been developed and validated. The developed assay shows selectivity of 100%, diagnostic sensitivity of 76% and limit of detection with 95% confidence interval in plant matrices ranging from 311 to 2,275 cells/mL of plant extracts. The assay was successfully used in a retrospective survey of selected host plants of relevance to Europe and environmental niches relevant to D. fangzhongdai. Samples of potato tubers and plants, plants from the Malinae subtribe (apple, pear, quince, and Asian pear tree) and fresh surface water from Slovenia were analyzed. D. fangzhongdai was not detected in any plant samples, however, 12% of surface water samples were found to be positive.
Ključne besede: molecular testing, diagnostics, plant pathogen, real-time PCR, Dickeya, survey, water
Objavljeno v DiRROS: 07.08.2024; Ogledov: 209; Prenosov: 151
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Povzetek: Purpose Hyporheic biofilms are the central site for biogeochemical cycling in streams and rivers. In view of global warming and increasing human pressures, this study aimed to compare the response of hyporheic biofilm biomass and activities from an unpolluted reference stream reach surrounded by forest with those from a stream reach exposed to agricultural and urban land use using a mesocosm experiment in which the water temperature and dissolved organic carbon (DOC) contents were manipulated. Methods Hyporheic sediments collected in the field from the two study reaches (i.e. reference and impacted) were incubated in the laboratory at two different temperatures (10 °C, 14 °C) and wetted with three types of synthetic water (control [C] – 0 mg L−1; low DOC – 5 mg L−1; high DOC – 30 mg L−1) for four weeks. The responses of the hyporheic biofilms were measured weekly using structural (total protein content [TPC] as a proxy for biofilm biomass) and functional measures (electron transport system activity [ETSA] and community-level physiological profiling [CLPP]). Results The response of hyporheic biofilms to temperature changes and DOC enrichment was site-specific for all studied measures (TPC, ETSA and CLPP, including measured average well colour development [AWCD]). The addition of DOC to biofilms from the pristine stream reach significantly heightened the responses at 10 °C, a temperature within the normal environmental temperature ranges of the reference location, but not at 14 °C, which was here, a temperature outside normal environmental range. On the other hand, biofilms from the impacted stream reach exhibited increased responses following DOC enrichment under both temperature regimes, with a particularly pronounced response at 14 ºC, in this case, both experimental temperatures were within the normal environmental temperature ranges of the study locations. Conclusion Hyporheic biofilms were shown to be, like benthic biofilms, sensitive to temperature changes and organic enrichment, but their response to temperature changes and enrichment caused by climate change and/or other anthropogenic pressures (i.e. point and non-point pollution, removal of the riparian zone, hydromorphological modifications, etc.) was not simply linear but site-specific. The intensity of the response, characterized by increased activity and biomass production, appears to be constrained within the temperature ranges prevalent in the environment from which the biofilms originate. These findings emphasize the importance of site-specific considerations in predicting the impacts of climate change and anthropogenic pressures on these critical components of river and stream ecosystems.
Ključne besede: sediments, respiration, enzymes, functional indicators, interactions
Objavljeno v DiRROS: 05.08.2024; Ogledov: 218; Prenosov: 211
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Povzetek: The increased globalization of crops production and processing industries also promotes the side-effects of more rapid and efficient spread of plant pathogens. To prevent the associated economic losses, and particularly those related to bacterial diseases where their management relies on removal of the infected material from production, simple, easy-to-perform, rapid and cost-effective tests are needed. Loop-mediated isothermal amplification (LAMP) assays that target 16S rRNA, fliC and egl genes were compared and evaluated as on-site applications. The assay with the best performance was that targeted to the egl gene, which shows high analytical specificity for diverse strains of the betaproteobacterium Ralstonia solanacearum, including its non-European and non-race 3 biovar 2 strains. The additional melting curve analysis provides confirmation of the test results. According to our extensive assessment, the egl LAMP assay requires minimum sample preparation (a few minutes of boiling) for the identification of pure cultures and ooze from symptomatic material, and it can also be used in a high-throughput format in the laboratory. This provides sensitive and reliable detection of R. solanacearum strains of different phylotypes.
Ključne besede: plant pathogens, bacterial diseases
Objavljeno v DiRROS: 02.08.2024; Ogledov: 236; Prenosov: 97
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