Biosurveillance of forest insects: part I—integration and application of genomic tools to the surveillance of non-native forest insects

Roe, Amanda D.; Torson, Alex S.; Bilodeau, Guillaume J.; Bilodeau, Pierre; Blackburn, Gwylim S.; Cui, Mingming; Cusson, Michel; Doucet, Daniel; Griess, Verena C.; Lafond, Valentine; Paradis, Gregory; Porth, Ilga; Prunier, Julien; Srivastava, Vivek; Tremblay, Émilie D.; Uzunovic, Adnan; Yemshanov, Denys; Hamelin, Richard

doi:10.1007/s10340-018-1027-4

Cited by 42 publications

(49 citation statements)

References 207 publications

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“…Accurate detection of invasive pathogens is a hallmark of efficient prevention and integrated pest management programs [42,43]. In some instance assessing pathogen viability may even be more crucial.…”

Section: Discussionmentioning

confidence: 99%

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

et al. 2020

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Wood and wood products can harbor microorganisms that can raise phytosanitary concerns in countries importing or exporting these products. To evaluate the efficacy of wood treatment on the survival of microorganisms of phytosanitary concern the method of choice is to grow microbes in petri dishes for subsequent identification. However, some plant pathogens are difficult or impossible to grow in axenic cultures. A molecular methodology capable of detecting living fungi and fungus-like organisms in situ can provide a solution. RNA represents the transcription of genes and can become rapidly unstable after cell death, providing a proxy measure of viability. We designed and used RNA-based molecular diagnostic assays targeting genes essential to vital processes and assessed their presence in wood colonized by fungi and oomycetes through reverse transcription and real-time polymerase chain reaction (PCR). A stability analysis was conducted by comparing the ratio of mRNA to gDNA over time following heat treatment of mycelial cultures of the Oomycete Phytophthora ramorum and the fungus Grosmannia clavigera. The real-time PCR results indicated that the DNA remained stable over a period of 10 days post treatment in heat-treated samples, whereas mRNA could not be detected after 24 hours for P. ramorum or 96 hours for G. clavigera. Therefore, this method provides a reliable way to evaluate the viability of these pathogens and offers a potential way to assess the effectiveness of existing and emerging wood treatments. This can have important phytosanitary impacts on assessing both timber and non-timber forest products of commercial value in international wood trade.

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Section: Discussionmentioning

confidence: 99%

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

et al. 2020

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“…Numerous molecular diagnostic tools have been developed in recent years for use in clinical settings, and there has been a push to apply similar tools to invasive species management. In particular, there are opportunities to use genomic tools for invasive species biosurveillance (e.g., for managing forest pests; Bilodeau et al 2018;Roe et al 2018). The use of deoxyribonucleic acid (DNA) for invasive species identification is well-established (Lyal and Miller 2019, this issue), but limited in application because relatively few species have been genetically sequenced and profiled in open access information systems, including GenBank, the National Institute of Health (NIH) annotated collection of all publicly available gene sequences (Benson et al 2013), or the other international databases with which GenBank interfaces (https://www.ncbi.nlm.nih.gov/genbank, accessed 30 October 2019).…”

Section: Genetic Detectionmentioning

confidence: 99%

Technology innovation: advancing capacities for the early detection of and rapid response to invasive species

et al. 2019

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The 2016-2018 National Invasive Species Council (NISC) Management Plan and Executive Order 13751 call for US federal agencies to foster technology development and application to address invasive species and their impacts. This paper complements and draws on an Innovation Summit, review of advanced biotechnologies applicable to invasive species management, and a survey of federal agencies that respond to these high-level directives. We provide an assessment of federal government capacities for the early detection of and rapid response to invasive species (EDRR) through advances in technology application; examples of emerging technologies for the detection, identification, reporting, and response to invasive species; and guidance for fostering further advancements in applicable technologies. Throughout the paper, we provide examples of how federal agencies are applying technologies to improve programmatic effectiveness and cost-efficiencies. We also highlight the outstanding technology-related needs identified by federal agencies to overcome barriers to enacting EDRR. Examples include improvements in research facility infrastructure, data mobilization across a wide range of invasive species parameters (from genetic to landscape scales), promotion of and support for filling key gaps in technological capacity (e.g., portable, field-ready devices with automated capacities), and greater investments in technology prizes and challenge competitions.

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“…The increase in DNA sequences in public databases, driven by advances in DNA sequencing technologies, has revolutionized the molecular diagnostics of pests and pathogens of crops and trees. Molecular identification and detection have become essential components of the prevention, mitigation and management toolbox of forest pests and pathogens [1,2]. DNA testing allows the rapid, sensitive and accurate detection of target organisms from small amounts of environmental samples harvested during surveys or inspections.…”

Section: Introductionmentioning

confidence: 99%

In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR

et al. 2020

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Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing to obtain accurate results from remote sites in real-time. This requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We developed a point-of-use real-time Polymerase Chain Reaction system using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions for on-site applications. We demonstrate the use of this approach with pathogens and pests covering a broad spectrum of known undesirable forest enemies: the fungi Sphaerulina musiva, Cronartium ribicola and Cronartium comandrae, the oomycete Phytophthora ramorum and the insect Lymantria dispar. We obtained positive DNA identification from a variety of different tissues, including infected leaves, pathogen spores, or insect legs and antenna. The assays were accurate and yielded no false positive nor negative. The shelf-life of the lyophilized reactions was confirmed after one year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable instruments demonstrate the suitability of the method, named in Situ Processing and Efficient Environmental Detection (iSPEED), for field testing. This kit fits in a backpack and can be carried to remote locations for accurate and rapid detection of pests and pathogens.

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Biosurveillance of forest insects: part I—integration and application of genomic tools to the surveillance of non-native forest insects

Cited by 42 publications

References 207 publications

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

Technology innovation: advancing capacities for the early detection of and rapid response to invasive species

In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR

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