Development and evaluation of a real‐time PCR seed lot screening method for Fusarium circinatum,causal agent of pitch canker disease

Fusarium circinatum is a serious pathogen of Pinus spp. worldwide, causing pitch canker disease. F. circinatum can contaminate seeds both internally and externally and is readily disseminated via contaminated seed. Many countries require screening of pine seeds for F. circinatum before they can be imported. The currently accepted screening method is based on culturing the pathogen on a semi‐selective medium and identifying it using morphological traits. This method is time‐consuming and does not allow for accurate identification of the pathogen to the species level. A bulk DNA extraction and real‐time PCR procedure to screen seeds for the presence of F. circinatum were developed in this study. The real‐time PCR method resulted in the detection of F. circinatum in 5 of 6 commercial seed lots tested and has a lower detection limit of 1 × 10^?5 ng of F. circinatum DNA per PCR. The culture‐based method detected Fusarium spp. in four of six of the same seed lots. The real‐time PCR method can be used to screen multiple seed lots in 2 days, whereas the culture‐based method requires a minimum of 1–2 weeks. This new real‐time PCR seed screening method allows for fast, sensitive and accurate screening and can be adapted to handle larger volumes of seeds.     

Pedicularis and Castilleja are natural hosts of Cronartium ribicola in North America: a first report

White pine blister rust disease, caused by the introduced pathogen Cronartium ribicola, has severely disrupted five‐needled pine ecosystems in North America. A 100‐year effort to manage this disease was predicated in part on the premise that the pathogen utilizes only species of Ribes (Grossulariaceae) as alternate hosts on this continent. The current study presents the first conclusive demonstration that some species in the family Orobanchaceae (Pedicularis racemosa and Castilleja miniata) are functioning as alternate hosts in a natural ecosystem of North America. This finding has implications for improving our understanding of epidemiology, pathogen adaptation and host–pathogen interactions within white pine blister rust.     

Detection method for Fusarium torreyae the canker pathogen of the critically endangered Florida torreya,Torreya taxifolia

Florida torreya (Torreya taxifolia Arn.) is an endangered conifer with a very limited range in the USA: two counties in Florida and one in Georgia, along the Apalachicola River. The species was once abundant in its small native range but suffered a major decline, ~99% loss, in the late 1950s to early 1960s that is thought to have been caused by a disease. Recently, a canker disease caused by Fusarium torreyae was identified as the primary cause of Florida torreya decline. Efforts to restore and preserve the species in situ and ex situ are hampered by lack of pathogen‐free planting stock, and there exists an interest in methods to verify pathogen presence in seeds and seedlings prior to collection and transport for planting. This paper presents a new species‐specific diagnostic method that enables detection of F. torreyae and may allow for conservation programmes to ensure germplasm is free of the pathogen prior to planting.     

Mechanisms and metabolomics of the host–pathogen interactions between Chestnut (Castanea species) and Chestnut blight (Cryphonectria parasitica)

Chestnut blight is a stem‐girdling disease of Castanea caused by the fungal pathogen Cryphonectria parasitica. Chestnut blight affects all Castanea species to some degree. In Asian species, chestnut blight is a commercially relevant disease which primarily affects nut production. In American and European species, chestnut blight has caused significant declines in wild populations and continues to negatively affect nut production in the European chestnut (C. sativa). Despite the profound effect of this disease in the Castanea genus, very little is known concerning the factors involved in the host–pathogen interaction between C. parasitica and its Castanea hosts. This review summarizes information on known mechanisms and metabolites involved in the host–pathogen interaction and contributes original information on the pathogen in relation to susceptible and putatively resistant genotypes with a view to furthering research that will promote a better understanding of this devastating disease and enable its control.     

A new method to detect Lonsdalea quercina in infected plant tissues by real‐time PCR

Presymptomatic and accurate diagnoses of pathogens are essential for disease prediction and the timely application of bactericide. The bacterium Lonsdalea quercina (=Brenneria quercina) has been reported as the causal agent of drippy nut and bark canker disease on oak in California (US) and Europe. In recent years, it is also found on Populus × euramericana trees in Henan province of China. This bacterium causes longitudinal cankers of a few centimetres in size on the bark surface of the upper trunk. In this study, we developed two species‐specific PCR assays using primer pairs LqfF/LqfR and LqgF/LqgR for the rapid and accurate detection of the pathogenic bacteria in diseased plant tissues. The results show that the LqfF/LqfR primers amplified only a single PCR band of approximately 382 bp and the LqgF/LqgR primers yielded a PCR product of approximately 286 bp. The two primers were successfully adapted to real‐time PCR based on SYBR Green I used with the ABI 7500 system. The detection limit of the reaction was 0.1 pg genomic DNA per 20 μl PCR reaction volumes. The pathogen was mainly detected in the phloem of cankers as well as in the exudates of diseased trees, but was not found in the xylem or leaves. The size of pathogen in distribution was larger than the lesion. The results demonstrate that real‐time PCR assays can be used to detect the pathogen by extracting DNA directly from infected plant tissues. This method is a rapid, reliable method for the presymptomatic and accurate detection of L. quercina, providing a useful insight into epidemiological studies.     

Quambalaria eucalypti a pathogen of Eucalyptus globulus newly reported in Portugal and in Europe

The Eucalyptus pathogen Quambalaria eucalypti has been reported from several subtropical and tropical countries of the Southern Hemisphere. During the course of a nationwide monitoring programme aimed at the detection of pathogens in commercial eucalypt plantations in Portugal, Q. eucalypti was found affecting Eucalyptus globulus. The identity of the pathogen was confirmed by sequence analyses of the internal transcribed spacer (ITS) region of the rDNA operon, as well as morphological characteristics. Quambalaria eucalypti is widespread throughout the eucalypt‐producing areas of Portugal. Pathogenicity studies revealed that different host genotypes showed various degrees of susceptibility to the pathogen. To our knowledge, this is the first report of Q. eucalypti on Eucalyptus spp. in Portugal and in the Northern Hemisphere.     

Assessment of molecular detection of Fusarium circinatum in insects and passive spore traps in Pinus radiata plantations

Fusarium circinatum is the causal agent of pitch canker, a destructive disease that threatens natural and planted pine forests around the world. Although pitch canker has caused problems in Spain and Portugal, concerning Europe as a whole, the fungus is not established across the pine distribution area. Its dispersion by wind and/or insect vectors could nevertheless play a role in the colonization of currently uninfected stands. It is therefore crucial to develop monitoring tools for its detection. To this end, we assessed the molecular detection of the pathogen in environmental samples of bark beetles and passive spore traps, collected in two infected Pinus radiata plantations in Basque country, Spain. The spread pattern of F. circinatum was assessed by an experimental design that included insect and spore traps installed at the centre, at the edge and outside the plots. Our results showed that F. circinatum was detected in both types of samples, at almost all collection dates. In both type of samples, positive detections were mainly found at the centre of the plots, a lower proportion at the edge, and very few outside. This suggests that long‐distance dispersion of Fusarium circinatum does not rely on wind spore dispersal neither on insect flight. Our study also shows that molecular methods are a powerful tool to monitor the pathogen in environmental samples.     

Rapid detection of Fusarium circinatum propagules on trapped pine beetles

Pitch canker is a destructive disease of pine caused by the fungus Fusarium circinatum. This taxon is listed as a quarantine fungus for several regional plant protection organizations throughout the world. Whereas long‐distance spread of the disease is made possible through the trade of infected pine seeds, local spread is caused by aerial dispersion or insect transportation of the fungal conidia. Developing a reliable and efficient tool to detect of F. circinatum in insects would be very useful to monitor the local spread of the pathogen. This tool would also provide the means to assess the range of insect species that could serve as potential vector of the fungus. A DNA extraction protocol was optimized and combined with a real‐time PCR test to detect F. circinatum on pine beetles. Using artificially contaminated Ips sexdentatus, it was shown that the test was able to detect down to 10 F. circinatum conidia per individual, and 20 conidia per batch of 10 insects, which is below the lowest inoculum load occurring in nature. With this technique, several batches of up to 10 insects may be analysed simultaneously, with a timescale for analysis reduced to <5 h and without the need for expertise in Fusarium taxonomy. This tool may be useful to monitor potential spread of the pathogen across regions. Using this method, to date, despite F. circinatum foci occurred in Northern Spanish regions across the border in France, the pathogen was not found on I. sexdentatus.     

An agglutination test for fast and specific detection of Erwinia psidii

Dieback and wilt, caused by Erwinia psidii (Ep), is one of the most important emergent diseases of Eucalyptus spp. in Brazil. Currently, pathogen detection relies on isolation of bacteria from infected plant tissue and either identification based on morphological, physiological and biochemical tests or DNA amplification using the polymerase chain reaction (PCR), which in many cases is laborious and cumbersome. Considering the need for a simpler and more rapid, yet reliable, method for detecting the pathogen, we obtained a polyclonal antibody (anti‐Ep) and developed an agglutination test for specific detection of E. psidii. The antiserum was produced against the E. psidii strain LPF534 and tested against 101 E. psidii isolates from Eucalyptus spp.; three E. psidii isolates from Psidium guajava; 23 Ralstonia solanacearum and 18 Xanthomonas axonopodis isolates pathogenic to Eucalyptus spp.; and seven endophytic isolates from Eucalyptus spp., three of which are phylogenetically related to the genus Erwinia. Results of direct ELISA indicated that a concentration as low as 3.5 µg/ml of the anti‐Ep antibody was able to detect the E. psidii antigen and that the antibody did not cross‐reacted with other bacteria pathogenic and non‐pathogenic to Eucalyptus spp. In the agglutination test, the anti‐Ep antibody showed positive reaction with all strains of E. psidii tested whereas cross‐reaction with none of the strains that belong to other taxonomic groups was observed. The agglutination test showed a detection limit of 10⁵ colony‐forming units (CFU)/ml, and its specificity was the same as that obtained by PCR amplification using E. psidii‐specific primers. These results demonstrate that the agglutination test developed here is a useful tool for specific, fast and inexpensive detection of E. psidii although only operational on pure bacterial suspensions and not yet directly from infected tissues.     

Widespread latent infection of Cryptostroma corticale in asymptomatic Acer pseudoplatanus as a risk for urban plantations

Sooty bark disease (SBD) caused by the pathogen Cryptostroma corticale is currently one of the risks to the population of Acer pseudoplatanus in Europe. After a number of records of symptomatic and dead trees in Prague, assessment of the latent non‐symptomatic stage of SBD was questioned as a means to forecast the health risk of the A. pseudoplatanus population. We used two methods of early detection of C. corticale in non‐symptomatic trees: cultivation from wood tissue on agar plates and a culture‐free approach based on nested PCR with newly designed species‐specific primers. The pathogen was detected in 25% of 112 examined trees from seven localities in Prague, but the disease incidence might be higher if more A. pseudoplatanus trees in Prague were included and if the crown infections were considered. The presence of C. corticale was positively correlated with discoloured wood, but its presence did not depend on the occurrence of external symptoms. Infected trees were more frequently found in groups on steep sites at higher elevations. In addition, heavier NO_x pollution combined with more paths and roads increased the incidence of C. corticale.     

Detection of Chalara fraxinea from tissue of Fraxinus excelsior using species‐specific ITS primers

Chalara fraxinea (teleomorph: Hymenoscyphus albidus) is known as a serious pathogen of Fraxinus excelsior, causing massive dieback of trees in Europe. The fungus is able to cause latent infections, and has been previously detected as an endophyte in asymptomatic tissues. Chalara fraxinea is a slow grower in culture, and is thus likely to be overgrown by faster growing fungi whenever pure culture isolations are being attempted. This study reports species‐specific ITS primers allowing fast and reliable detection of the pathogen directly from infected tissues of F. excelsior.     

Direct quantitative real‐time PCR assay for detection of the emerging pathogen Neonectria neomacrospora

The epidemic outbreak in northern Europe of Neonectria neomacrospora, the causal agent of dieback in Abies spp., led the European and Mediterranean Plant Protection Organization (EPPO) to include the pathogen on its alert list in 2017. Effective monitoring of this pathogen calls for a rapid and sensitive method of identification and quantification. A probe‐based real‐time PCR (qPCR) assay based on the β‐tubulin gene was developed for the detection and quantification of N. neomacrospora in infected wood samples, and directly for ascospores. This study presents the first published species–specific molecular detection assay for N. neomacrospora. The analytical specificity was validated on taxonomically closely related fungal species as well as on 18 fungal species associated with the host (Abies sp.). The analytical sensitivity was tested on naturally infected wood, on purified pathogen DNA in a matrix of host DNA and on N. neomacrospora ascospores for detection of airborne inoculum. The latter was tested both with a DNA extraction step prior to qPCR and without DNA extraction by direct qPCR on collected ascospores. The assay was specific to N. neomacrospora, with a sensitivity of 130 fg purified DNA, or 10 ascospores by direct qPCR. Omitting DNA extraction and amplifying directly on unpurified ascospores improved assay sensitivity significantly.     

Infection approach of Diplodia sapinea,the causal agent of tip blight of Pinus tabulaeformis in China

To clarify the infection approach of Diplodia sapinea, a pathogen that causes tip blight of Pinus tabulaeformis, the infection process of the pathogen in needles was observed using scanning electron microscopy (SEM). In addition, the disease incidence on branches damaged by Aphrophora flavipes (Hemiptera: Cercopidae) and Dioryctria splendidella (Lepidoptera: Pyralidae) in the forest was also investigated. Then, branches and needles of P. tabulaeformis were inoculated using the D. sapinea spore suspension under indoor and field conditions. The results showed that the damage caused by A. flavipes could aggravate the occurrence of tip blight of P. tabulaeformis to some extent. Moreover, the pathogen could also penetrate 1‐, 2‐ and 3‐year‐old pine needles through stomata in the field. The pathogen infected the 1‐year‐old branches first and then gradually spread to 2‐ and 3‐year‐old branches.     

The Eucalyptus stem canker pathogen Teratosphaeria gauchensis represents distinct genetic groups in Africa and South America

Teratosphaeria gauchensis (Capnodiales) causes a serious stem canker disease on commercially propagated Eucalyptus species in South America. Recently, this pathogen was detected for the first time in Africa. Very little is known regarding the biology or origin of T. gauchensis, but it has been suggested that it is native to South America. The aim of this study was to compare isolates from Africa and South America using microsatellite markers. Bayesian analysis conducted in STRUCTURE, principal coordinates analysis and a UPGMA dendrogram revealed two distinct genetic groups for these isolates. The South American isolates were more genetically diverse than those from Africa. Patterns of genetic diversity in Africa suggest that T. gauchensis could have been introduced into Zimbabwe before spreading north‐eastwards. The existence of the two genetic groups and high haplotype richness associated with the South American and Zimbabwean populations suggest that it will be more difficult to reduce the impact of disease caused by T. gauchensis in these regions than in those areas where there is limited genetic diversity.     

Conifer species influence Heterobasidion irregulare sporulation on stem discs exposed to natural inoculum and root wood decay in soil‐block tests

The fungal pathogen Heterobasidion irregulare has caused substantial damage to pine species in much of the south‐eastern United States, but the potential for damage from Heterobasidion root disease to forest tree species of the Great Lakes Region has not been thoroughly investigated. In each of three trials in two infested stands, fresh stem discs of six native conifer species were exposed to natural inoculum and examined for the asexual Spiniger stage of H. irregulare after incubation in the laboratory. In the first trial, the fungus was infrequently observed on discs, and differences among species were not found. But in the other two trials, detection of the pathogen was much more frequent on discs of tamarack (Larix laricina), red pine (Pinus resinosa) and white spruce (Picea glauca) than those of northern white cedar (Thuja occidentalis), eastern hemlock (Tsuga canadensis) and balsam fir (Abies balsamea). In a second study, the ability of an isolate of H. irregulare to decay root sapwood of these same species was compared using a soil‐block decay test. After 16 weeks of incubation, weight loss due to decay was greatest for red pine (23.2%) and larch (19.1%) and least for balsam fir (1.3%). Differences in the ability of H. irregulare to infect and saprophytically utilize substrate of these important tree species should prompt additional investigation of the relative risk posed to forests of the Great Lakes Region.     

Extent of colonization by Raffaelea quercivora of artificially inoculated living and gamma‐ray‐sterilized seedlings of two Japanese and three American oak species

Mass mortality of Fagacean tree species caused by Raffaelea quercivora has occurred widely in Japan. Because conidia or other propagules of the pathogen have not been found in infected trees, pathogen spread is assumed to occur primarily by hyphae. To clarify the relationship between hyphal growth of the pathogen within trees and their vessel arrangements, we examined two native Japanese oaks, Quercus crispula and Quercus glauca, and three exotic American oaks, Quercus coccinea, Quercus palustris and Quercus rubra. Quercus glauca is a radial‐porous species, whereas the other four species have a ring‐porous wood structure. Hyphal growth within inoculated potted living seedlings and in cut, sterilized stem segments of these species was examined microscopically after fungal inoculation. Water conductance in the seedlings was examined using transverse stem sections. The proportion of non‐conductive sapwood in Q. crispula, Q. coccinea and Q. palustris differed between inoculation and control treatment, being much higher in inoculated seedlings. The proportions were positively correlated with the extent of the hyphal growth. In sterilized stem segments, the extent of fungal colonization varied among the foreign ring‐porous species Q. coccinea, Q. palustris and Q. rubra. It is hypothesized that the extent of colonization by R. quercivora reflects the extent of non‐conductive sapwood irrespective of tree species, but is little affected by vessel arrangements.     

Rapid and accurate detection of Ceratocystis fagacearum from stained wood and soil by nested and real‐time PCR

A nested and real‐time PCR assay was developed for the rapid and accurate detection of Ceratocystis fagacearum, which is the causal agent of oak wilt in stained wood and soil. Based on the differences of the internal transcribed spacer (ITS) sequences of Ceratocystis spp., one pair of species‐specific primers, CF01/CF02, was designed. Whereas a 280‐bp product was amplified using the purified DNA from three isolates of C. fagacearum as the template, no PCR product was obtained from template of other 18 fungi. The detection sensitivity was 10 pg genomic DNA per 25‐μl PCR reaction volume. To increase detection sensitivity, a nested PCR was developed by using ITS1/ITS4 as the first‐round primers and CF01/CF02 in the second round, as it can detect 1 pg genomic DNA per 25‐μl PCR reaction volume. More importantly, CF01/CF02 primers were successfully adapted to real‐time PCR with a detection limit of 0.1 pg genomic DNA per 20‐μl PCR reaction volume. Using these two methods, we could rapidly and accurately detect the pathogen in artificially infected wood and soil.     

Assessment of the eradication measures applied to Phytophthora ramorum in Irish Larix kaempferi forests

Phytophthora ramorum is the causal agent of the sudden larch death epidemic in Ireland and the UK. Within the EU, it is a quarantine pathogen and eradication measures are required if it is detected in horticultural or forest environments. Eradication measures in forests include the clearance of susceptible tree hosts from the infected stand along with all host known to support pathogen sporulation within a 250‐m buffer zone of the infected stand. Between 2010 and 2016, these measures have affected over 18,000 ha of Larix kaempferi forests in Ireland and the UK, but the epidemic continues to spread. An assessment of the efficacy of the eradication measures has not been published to date. Here, we provide details of the detection frequency of P. ramorum from aerial (rainwater) and terrestrial (soil, watercourses, plant material) sources in three forest locations in Ireland that had significant areas of L. kaempferi affected by P. ramorum before their removal. Monitoring of six plots with differing infection and eradication management histories was carried out from September 2013 to 2015. Presence of P. ramorum was confirmed by plating plant material onto selective media, followed by morphological identification. Phytophthora ramorum was detected in 65 of 1283 samples, in all sample types and in 17 of the 20 months sampled. Only three of the 295 soil samples were positive for P. ramorum, with all of these coming from an area under perennial standing water. The most positive samples came from a plot where symptomatic Larix trees had not been removed and the findings occurred consistently over the 2‐year study. Plots where infected Larix had been removed were rarely positive for P. ramorum across all the sample types indicating a level of success from the eradication measures in reducing pathogen levels on the sites.     

Susceptibility of six pine species to Gremmeniella abietina isolates from Spain

Inoculation experiments were performed in order to evaluate the virulence of Gremmeniella abietina isolates from Spain on the main pine species planted in the Iberian Peninsula, as well as the influence of seedling age on this virulence. Two different experiments were carried out with four isolates of G. abietina from Spain. The greenhouse experiments consisted of seedling inoculations. One‐ and 2‐year‐old seedlings of the following five pine species were used: Pinus halepensis, Pinus pinea, Pinus pinaster, Pinus sylvestris and Pinus uncinata; also, 1‐year‐old seedlings of P. nigra were inoculated. The relative necrosis length (RNL) caused by the pathogen after 130 days was used as a response variable. The laboratory experiments were performed on 2‐ to 6‐year‐old internodes of the above pine species excluding P. uncinata. The necrosis length after 6 weeks of incubation was measured. The results have shown that all G. abietina isolates were pathogens on seedlings of these six pine species and seedlings of P. halepensis were consistently the most susceptible ones, although it is important to take into account that all the isolates used in the present work were isolated from P. halepensis, the only pine species in Spain where G. abietina has been recovered up to now. The susceptibility of the other pine species depended on the age of the seedlings.