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

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.

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens.

Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.

Molecular Detection of 10 of the Most Unwanted Alien Forest Pathogens in Canada Using Real-Time PCR.

Invasive alien tree pathogens can cause significant economic losses as well as large-scale damage to natural ecosystems. Early detection to prevent their establishment and spread is an important approach used by several national plant protection organizations (NPPOs). Molecular detection tools targeting 10 of the most unwanted alien forest pathogens in Canada were developed as part of the TAIGA project (http://taigaforesthealth.com/). Forest pathogens were selected following an independent prioritization. Specific TaqMan real-time PCR detection assays were designed to function under homogeneous conditions so that they may be used in 96- or 384-well plate format arrays for high-throughput testing of large numbers of samples against multiple targets. Assays were validated for 1) specificity, 2) sensitivity, 3) precision, and 4) robustness on environmental samples. All assays were highly specific when evaluated against a panel of pure cultures of target and phylogenetically closely-related species. Sensitivity, evaluated by assessing the limit of detection (with a threshold of 95% of positive samples), was found to be between one and ten target gene region copies. Precision or repeatability of each assay revealed a mean coefficient of variation of 3.4%. All assays successfully allowed detection of target pathogen on positive environmental samples, without any non-specific amplification. These molecular detection tools will allow for rapid and reliable detection of 10 of the most unwanted alien forest pathogens in Canada.

Appropriateness of probit-9 in the development of quarantine treatments for timber and timber commodities.

Following the increasing international phasing out of methyl bromide for quarantine purposes, the development of alternative treatments for timber pests becomes imperative. The international accreditation of new quarantine treatments requires verification standards that give confidence in the effectiveness of a treatment. Probit-9 mortality is a standard for treatment effectiveness that has its origin in fruit fly research, and has been adopted by the United States Department of Agriculture for fruit flies and several other pests. Following this, the probit-9 standard has been adopted as a benchmark for many quarantine treatments worldwide. This article discusses aspects of the application of this concept for a range of timber pests. Problematic issues include the often small pest populations available for testing, the limits of modeling pest responses to a treatment in the absence of sufficient numbers for treatment verification, the species diversity of pests and host materials and the physical and chemical conditions of host material or treatment conditions. Where treatment verification by killing large numbers of individuals is impossible, data collected from small populations or under specific conditions must be interpreted with caution. We discuss possible alternative approaches to probit-9 as a treatment efficacy standard.

Lethal temperature for pinewood nematode, Bursaphelenchus xylophilus, in infested wood using microwave energy.

To reduce the risks associated with global transport of wood infested with pinewood nematode Bursaphelenchus xylophilus, microwave irradiation was tested at 14 temperatures in replicated wood samples to determine the temperature that would kill 99.9968% of nematodes in a sample of ≥ 100,000 organisms, meeting a level of efficacy of Probit 9. Treatment of these heavily infested wood samples (mean of > 1,000 nematodes/g of sapwood) produced 100% mortality at 56 °C and above, held for 1 min. Because this "brute force" approach to Probit 9 treats individual nematodes as the observational unit regardless of the number of wood samples it takes to treat this number of organisms, we also used a modeling approach. The best fit was to a Probit function, which estimated lethal temperature at 62.2 (95% confidence interval 59.0-70.0) °C. This discrepancy between the observed and predicted temperature to achieve Probit 9 efficacy may have been the result of an inherently limited sample size when predicting the true mean from the total population. The rate of temperature increase in the small wood samples (rise time) did not affect final nematode mortality at 56 °C. In addition, microwave treatment of industrial size, infested wood blocks killed 100% of > 200,000 nematodes at ≥ 56 °C held for 1 min in replicated wood samples. The 3(rd)-stage juvenile (J3) of the nematode, that is resistant to cold temperatures and desiccation, was abundant in our wood samples and did not show any resistance to microwave treatment. Regression analysis of internal wood temperatures as a function of surface temperature produced a regression equation that could be used with a relatively high degree of accuracy to predict internal wood temperatures, under the conditions of this study. These results provide strong evidence of the ability of microwave treatment to successfully eradicate B. xylophilus in infested wood at or above 56 °C held for 1 min.

Ophiostomatoid fungi associated with the northern spruce engraver, Ips perturbatus, in western Canada.

A number of ophiostomatoid fungi were isolated from the spruce-infesting bark beetle, Ips perturbatus and its galleries collected from felled spruce trees and logs in northern BC and the Yukon Territory. Isolates were identified to species using morphological characteristics, nuclear ribosomal DNA and partial beta-tubulin gene sequences. Thirteen morphological and phylogenetic species were identified among the isolates. Leptographium fruticetum, Leptographium abietinum, Ophiostoma bicolor, Ophiostoma manitobense, O. piceaperdum, and eight undescribed species of the genus Ophiostoma and the anamorph genera Leptographium, Hyalorhinocladiella, Ambrosiella and Graphium. A number of these species, i.e. L. fruticetum, Hyalorhinocladiella sp. 2, O. bicolor and O. manitobense, were isolated repeatedly from I. perturbatus, while others, i.e. Graphium sp. 1 and O. piceaperdum, seemed to be sporadic associates. Among all the isolates, L. fruticetum had the highest relative dominance in this survey. A high frequency of occurrence of this species with the beetle may indicate a specific relationship between the two partners.

Ophiostoma breviusculum sp. nov. (Ophiostomatales, Ascomycota) is a new species in the Ophiostoma piceae complex associated with bark beetles infesting larch in Japan.

A new species of the Ophiostoma piceae-complex was isolated from bark beetles and the insect galleries of Larix kaempferi in Japan. This species was described as Ophiostoma breviusculum. The fungus was morphologically similar to O. piceae and O. quercus. However the average length of the perithecial necks and synnemata were shorter than for O. piceae and O. quercus. Synnemata morphological characteristics also differentiated O. breviusculum from the other species of the Ophiostoma piceae-complex isolated from conifers. Mating tests demonstrated that this fungus did not produce perithecia with O. floccosum, O. piceae and O. quercus. In phylogenetic trees using rDNA ITS O. breviusculum was placed in a clade with O. canum, O. piceae and O. subalpinum, but when using beta-tubulin it was placed into a separate clade.