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Effective detection of pathogens from complex substrates is a challenging task. Molecular approaches such as real-time PCR can detect pathogens present even in low quantities. However, weak real-time PCR signals, as represented by high cycle threshold ( Ct) values, may be questionable. Therefore, setting a reliable Ct threshold to declare a positive reaction is important for specific detection. In this study, five methods were assessed for their performance in determining a Ct cut-off value. These methods were based on the widely used probability of detection ( POD) or receiver-operating characteristic ( ROC) approaches. Two important forest pathogens, Hymenoscyphus fraxineus and Fusarium circinatum, were used to set up three experimental frameworks that combined two types of substrates (seed lots and spore traps) and different PCR machines. The ROC-based method emerged as the most complete and flexible method under various experimental conditions. It was demonstrated that the ROC method leads to a cut-off value below which late Ct results can reliably be considered indicative of positive test results. This cut-off value must be determined for each experimental approach used. The method based on the distribution of a previously determined set of Ct values corresponding to false-positives appeared to be better adapted to detecting false-negative results, and thus useful for testing potentially invasive pathogens. [ABSTRACT FROM AUTHOR]

Hymenoscyphus fraxineus is an invasive fungus in Europe and causes a severe decline affecting ash, which began in the late 1990s. One of the symptoms associated with the disease is lesions in the outer bark of the collar area. However, the aetiology of these basal lesions, and in particular the relative roles of H. fraxineus and Armillaria species, is still controversial; moreover, little is known about the influence of environmental factors on the disease epidemiology. This study therefore surveyed 42 plots located in northeastern France, in an area affected by ash decline since 2008, in order to determine which environmental factors condition the severity of lesions associated with H. fraxineus on ash collar. The spatial pattern that is a consequence of the invasive spread of the disease was taken into account in the analysis, using a spatial hierarchical Bayesian model fitted by integrated nested laplace approximation ( INLA). Results show that while basal lesions are tightly associated with H. fraxineus, their severity is influenced by the Armillaria species present in the plot. Sites with vegetation indicating moist conditions, or more humid topographical positions, were associated with more developed basal lesions. [ABSTRACT FROM AUTHOR]

This article discusses the susceptibility of red oak seedlings and chestnut seedlings to phytophthora cinnamomi, a fungal agent. The dynamics of infection have been examined in plant material raised in a rhizotron. In the oak species, primary root tissues were susceptible whereas secondary cortical tissues showed some resistance to phytophthora cinnamomi. Secondary cortical tissues of the tap root in chestnut seedlings were susceptible. Inoculations with phytophthora cinnamomi were performed both in situ and on excised roots of mature oak seedlings. In both cases, the resistance of oak roots and shoots was negatively correlated with diameter at the inoculation point. Small roots were resistant, whereas collar and trunk were susceptible. In contrast to oak, small excised roots of mature chestnut were susceptible to phytophthora cinnamomi.

The globalization in plant material trading has caused the emergence of invasive pests in many ecosystems, such as the alder pathogen Phytophthora ×alni in European riparian forests. Due to the ecological importance of alder to the functioning of rivers and the increasing incidence of P. ×alni-induced alder decline, effective and accessible decision tools are required to help managers and stakeholders control the disease. This study proposes a Bayesian belief network methodology to integrate diverse information on the factors affecting the survival and infection ability of P. ×alni in riparian habitats to help predict and manage disease incidence. The resulting Alder Decline Network (ADnet) management tool integrates information about alder decline from scientific literature, expert knowledge and empirical data. Expert knowledge was gathered through elicitation techniques that included 19 experts from 12 institutions and 8 countries. An original dataset was created covering 1189 European locations, from which P. ×alni occurrence was modeled based on bioclimatic variables. ADnet uncertainty was evaluated through its sensitivity to changes in states and three scenario analyses. The ADnet tool indicated that mild temperatures and high precipitation are key factors favoring pathogen survival. Flood timing, water velocity, and soil type have the strongest influence on disease incidence. ADnet can support ecosystem management decisions and knowledge transfer to address P. ×alni-induced alder decline at local or regional levels across Europe. Management actions such as avoiding the planting of potentially infected trees or removing man-made structures that increase the flooding period in disease-affected sites could decrease the incidence of alder disease in riparian forests and limit its spread. The coverage of the ADnet tool can be expanded by updating data on the pathogen's occurrence, particularly from its distributional limits. Research on the role of genetic variability in alder susceptibility and pathogen virulence may also help improve future ADnet versions., Competing Interests: Declaration of competing interest The authors have no competing interests to declare that are relevant to the content of this article., (Copyright © 2024. Published by Elsevier B.V.)