Plant Pathology

Management of widespread plant pathogens is challenging as climatic differences among crop growing regions may alter key aspects of pathogen spread and disease severity. Xylella fastidiosa is a xylem-limited bacterial pathogen that is transmitted by xylem sap feeding insects. Geographic distribution of X. fastidiosa is limited by winter climate and vines infected with X. fastidiosa can recover from infection when held at cold temperatures. California has a long history of research on Pierces disease, and significant geographic and climatic diversity among grape-growing regions. This background in combination with experimental disease studies under controlled temperature conditions can inform risk assessment for X. fastidiosa spread and epidemic severity across different regions and under changing climate conditions. Californias grape growing regions have considerable differences in summer and winter climate. In northern and coastal regions, summers are mild and winters cool, conditions favoring winter recovery of infected vines. In contrast, in inland and southern areas summers are hot and winters mild, reducing likelihood of winter recovery. Here, winter recovery of three table grape cultivars (Flame, Scarlet Royal, and Thompson seedless) and three wine grape cultivars (Sauvignon Blanc, Cabernet Sauvignon, and Zinfandel) were evaluated under temperature conditions representative of the San Joaquin Valley, an area with hot summers and mild winters that has been severely impacted by Pierces disease, and contains a large portion of California grape production. Mechanically inoculated vines were held in the greenhouse under one of three warming treatments to represent different seasonal inoculation dates prior to being moved into a cold chamber. Winter recovery under all treatments was generally limited, but with some cultivar variation. Given hot summer temperatures of many grape-growing regions worldwide, as well as increasing global temperatures overall, winter recovery of grapevines should not be considered a key factor affecting X. fastidiosa spread and epidemic severity in the majority of cases.

Monitoring virulent strains within fungal pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in genomes based on high-throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms and in planta phenotyping remains necessary. We developed a method for bulk phenotyping on checkerboard microcanopies of wheat near-isogenic lines (BPC) for estimating the frequency of virulence against an Stb gene in populations of Zymoseptoria tritici, the causal agent of Septoria tritici blotch in wheat, without the need for strain-by-strain phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines - one with the resistance gene and the other without it - with a multi-strain cocktail representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using Stb16q, a resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, and synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with recently developed molecular methods.

In the context of global warming, it is crucial to focus on the effects of temperature on the emergence of new lineages of endemic pathogen species, such as Puccinia striiformis f. sp. tritici (Pst) the causal agent of yellow rust on wheat. We characterized the thermal aptitude of representative isolates from the most recent common European Pst races. We assessed two key aggressiveness components - infection efficiency (IE) and latency period (LP) - under warm and cold thermal regimes, comparing 10 Pst isolates collected from 2010 to 2020 with three "old" reference isolates. The significant differences observed suggest that this species has the potential to adapt to temperature changes, but that such adaptation probably did not drive the establishment of the most recent races and the dominant Warrior and Warrior(-) they succeeded. These races display "generalist" behavior with respect to temperature, with Warrior(-) showing no more aggressiveness than the races replaced since the 1990s. The differences in competitive success between emerging Pst lineages are probably due to the deployment of resistance genes in wheat and the advantages of new forms of virulence emerging independently of thermal adaptability. However, variations in thermal adaptability for both aggressiveness components suggested an impact of geographic origin within the Warrior and Warrior(-) races, as previously reported for the "old" reference isolates. Furthermore, the independence of thermal adaptability established for IE and LP implies that the effects of temperature may depend on the stage of the epidemic (early or late), potentially modifying seasonal dynamics.

Small-spored Alternaria species such as A. alternata and A. arborescens are frequently isolated from diseased potato and tomato plants. However, their respective host ranges and pathogenic behaviours remain poorly resolved, and it is unclear whether their occurrence across hosts reflects true specialisation or ecological opportunism. Limited genetic differentiation among these closely related taxa further complicates their classification as primary necrotrophs or secondary colonisers. In this study, we analysed natural populations of small-spored Alternaria from Germany, Poland, and Serbia using molecular phylogenetics, morphological characterisation, and controlled infection assays to clarify species identity, host associations, and pathogenic potential. Both A. alternata and A. arborescens were detected across all regions and hosts, indicating broad distribution and ecological overlap. The two species were consistently isolated from foliar lesions and were each capable of causing characteristic Alternaria Brown-Spot (ABS) symptoms, thereby fulfilling Kochs postulates. Phylogenetic analyses based on Alt A1 and RPB2 loci resolved two well-supported species clades and revealed extensive haplotype sharing across more than 1300 km, multiple hosts, and diverse climates, suggesting high gene flow and limited population structure. The consistent co-occurrence and comparable pathogenicity of A. alternata and A. arborescens underscore their equal ecological relevance and redefine their roles in ABS epidemiology. These findings indicate that perceived differences in host specialisation may be overstated and that both species contribute equally to Alternaria Brown-Spot epidemics in solanaceous crops.

Blackleg disease in potato, caused by soft rot Pectobacteriaceae, is a substantial cause of loss in seed potato production. Recent research has attempted to identify bacteria with antagonistic activity against several diseases, among which blackleg. However, most biocontrol agents have been tested only in-vitro or in the greenhouse. In this study, we tested the effect of bacterial biocontrol agents in a four-year field experiment against blackleg caused by Pectobacterium brasiliense and Dickeya solani. Effects of the treatments on disease incidence was highly variable between years and also differed between cultivars, soil type and even replicates. Disease incidence was on average higher in sandy soil compared to clay soil and higher in the cultivar Kondor than Mozart. For a subset of the bacterial isolates genome mining could detect the presence of genes involved in the production of antibiotics and siderophores, but this was not correlated with disease incidence in the field. Moreover, most isolates were able to survive in storage on tubers from inoculation until planting. Thus, we conclude that while the used isolates showed the potential for antagonistic activity and were present on tubers when planting, no antagonist treatment could consistently decrease disease incidence. Inoculation of the isolates on the tuber surface might have been insufficient for plant colonization.

Phytophthora agathidicida, a plant pathogenic oomycete, causes fatal dieback disease in New Zealand kauri trees (Agathis australis). Currently, few treatments exist to prevent or cure this infection. Previous research has demonstrated the potent in vitro inhibition of multiple lifecycle stages of P. agathidicida by the oomycide oxathiapiprolin. In this study, we have evaluated the efficacy of oxathiapiprolin in planta as either a protective or curative treatment. Kauri seedlings (1-2 years old) were treated with 10 or 50 mg of oxathiapiprolin, in the form of Zorvec Enicade, per seedling as a soil drench either before (7 days) or after (15 days) inoculation with P. agathidicida NZFS 3770 to test for protective and curative activities, respectively. Results showed that oxathiapiprolin treatments successfully protected the kauri seedlings from disease, with the higher dose (50 mg) demonstrating greater efficacy. However, the treatments did not cure kauri seedlings already infected withP. agathidicida, likely because the infection was already well-established by the time of treatment. This study demonstrates that, while oxathiapiprolin shows protective effects against P. agathidicida infection in kauri seedlings, its lack of curative properties significantly limits its potential as a practical tool for managing kauri dieback disease.

Invasive pathogens are a major threat to forest health especially in managed forest with low diversity. The die-back of European Fraxinus spp. caused by the fungus Hymenoscyphus fraxineus is the latest example of pathogen invasion causing widespread damage. Host resistance and environment, in particular stand factors were shown to strongly impact disease severity on European ash. The fact that H. fraxineus reproduce mostly through heterothallic sexual reproduction suggest that an Allee effect could limit the mating success at low host densities, thus limiting inoculum production and disease development. Populations of H. fraxineus were monitored during the fruiting period in a network of stands across a host density gradient in forest and non-forest environment. Ash dieback, basal area of ash, density of infected ash leaf debris (rachis) and apothecia in the litter and ascospores load in the air were determined in the different environments during two years. We showed significant differences between forest and non-forest environment with ash dieback, infection rate and inoculum production higher in forest settings. Host density significantly affected disease development, with crown dieback, density of infected rachis in the litter and inoculum production increasing with host density. We also demonstrated that fruiting rate, i.e. the number of apothecia per infected rachis dry weight, is strongly dependent on infected rachis density. Inoculum production is therefore limited at low host densities. Such a component Allee effect could be important in H. fraxineus epidemiology and invasion dynamic.

Phytophthora ramorum (Pr) is an invasive oomycete in Europe and North America and the causal agent of sudden oak death (SOD), which occurs along the coastal fog belt of California and southwestern Oregon, and it also causes sudden larch death in the UK. The Macaronesian laurel forest (MLF), a relict subtropical evergreen forest of the North Atlantic islands, shares climatic and some taxonomic affinities with those areas affected by SOD. To assess the disease risk, we tested the foliage susceptibility of MLF species and their capacity to sustain Pr sporulation and compared the climatic suitability with other areas where the pathogen is established. Detached leaves of 15 species were inoculated with zoospores and mycelium (through wounding) with five Pr isolates belonging to the EU1 and NA1 clonal lineages. MLF species showed diverse responses to Pr, ranging from extensive necroses on Viburnum tinus to asymptomatic sporulation on Picconia excelsa. Eleven species developed necrotic lesions to different degrees through zoospore inoculation while this increased to 13 species through wound treatment. Overall, small necrotic lesions (i.e. tolerance) were predominant, but Pr was rather aggressive to V. tinus, Arbutus canariensis and Ilex canariensis. Although the mean sporangial production was generally low (25-201 sporangia) in all species, the number of sporangia per leaf in five MLF species was similar to those reported for Umbellularia californica, a key host driving the SOD epidemics in California. Climatic suitability indexes in MLF areas were similar to those where SOD is found in California. Our results indicate a moderate to high risk of Pr establishment if the pathogen is introduced in the MLF.

To quantify the relationship between grapevine disease severity and crop losses at the plant scale, we conducted a three-year field experiment at two sites near Bordeaux (France), surveying mildews and rots on both foliage and clusters. A first set of analysis indicated that only downy mildew (DM) significantly affects yield (mass of grape clusters harvested) in our experimental conditions. We then leverage this situation to model the relationship between DM severity (measured by standardized AUDPC) and yield losses at vine stock scale. For AUDPC ranging from 0 to 10%, an increase of the severity of DM of 1% on the clusters decrease yield by 2% regardless of years and sites. These values ranges from 1.1% to 9% when considering the severity of DM on the foliage, depending on sites and years. This variability was correlated with a moisture risk index calculated between crop stages inflorescences visibles to pre-ripening of the berries. An increase of the severity of DM of 1% on the foliage decreases yield by 1.2% during dry year (quantile 10% of the index), by 3.3% during intermediate year (median the index) and by 7.3% during wet year (quantile 90% of the index). An important perspective will be to fit and validate the proposed statistical models with datasets covering a broader range of climatic, geographic and agronomic conditions, including the characterization of cultivar-specific responses.

Invasive fungal diseases represent a major threat to forest ecosystems worldwide. As fungicides are often unfeasible and not a sustainable solution, only a few other control options are available, including biological control. In this context, the use of parasitic mycoviruses as biocontrol agents of fungal pathogens has recently gained particular attention. Since the 1990s, the Asian fungus Hymenoscyphus fraxineus has been causing lethal ash dieback across Europe. In the present study, we investigated the biocontrol potential of the mitovirus Hymenoscyphus fraxineus mitovirus 2 (HfMV2) previously identified in Japanese populations of the pathogen. HfMV2 could be successfully introduced via co-culturing into 16 out of 105 virus-free isolates. A virus infection had contrasting effects on fungal growth in vitro, from cryptic to detrimental or beneficial. Virus-infected H. fraxineus isolates whose growth was reduced by HfMV2 showed a lower virulence on ash (Fraxinus excelsior) saplings compared to their isogenic virus-free isolates. The results suggest that mycoviruses exist in the native populations of H. fraxineus in Asia that have the potential for biological control of ash dieback in Europe.

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are to some degree all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomato, several species cause early blight, leaf spot, and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides, and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem on cultivated tomato, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant-pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.

The potential of the invasive spotted lanternfly (Lycorma delicatula White; SLF) to serve as vector of plant pathogens is especially a concern for grapevine growers, as SLF are known to invade and can heavily infest vineyards, where the insects may encounter grapevines with multiple diseases. In this study, we have found that, when given the choice, SLF preferentially fed on healthy vines and that, when forced, feeding on Pierces disease (PD)-infected vines had negative effects on nymph development. Upon transmission trials, most of the recipient vines showed scorching symptoms typical of PD and one of the recipient vines resulted positive by qPCR. Our study suggests that SLF could be a vector of PD, however further experiments are needed to determine if transmission would occur under field conditions.

The characterization of virulence frequencies has to be regularly updated to identify which genes are currently efficient and use this information to advise gene deployment by choosing varieties depending on the current composition of local pathogen population. In L. maculans on Brassica napus, because different genes were characterized by different teams, because new interactions are continuously identified and seed of differentials are difficult to obtain, we today still lack isolates characterized on all current resistance genes. On the one hand, we assembled a set of 12 isolates characterized on 13 of the 17 described resistance genes, having clearly compatible and clearly incompatible isolates for each interaction. This set can be used to characterize the L. maculans - B. napus interaction at cotyledon stage. Expanding the set of isolates with clearly virulent ones allowed us to detect inconsistent behaviour or intermediate (avirulent) phenotypes. On the other hand, we used this set of isolates as controls to identify virulence frequencies in a current French L. maculans population sampled in 2018 at Le Rheu. We provide the current status for 13 avirulence frequencies, including LepR1, LepR2 and LepR3 available in near isogenic lines of spring canola but not yet documented in France. Avirulence frequencies on the genes Rlm1, Rlm2, Rlm3, Rlm4, Rlm7, Rlm9 and LepR3 were low, indicating the lack of efficacy of these genes against the current population. In the opposite, all or most of isolates were avirulent for the genes Rlm5, Rlm6, Rlm10, Rlm11, LepR1 and LepR2. An optimistic point of view could conclude that there are ample resources for oilseed rape breeding. However, as compared to previous studies, so far all the resistance genes used on significant acreage without additional management practices have lost efficacy and only avirulences corresponding to resistance genes not deployed in France retain efficacy. While the call to wisely manage the available host resistance genes is not recent, it is still relevant. Adding, management practices to the deployment of resistance genes in order to reduce inoculum carry-over from one growing season to the next and to lower population sizes is key to maintain their efficacy over time.

Christmas trees are an economically and culturally important ornamental plant in North America. Many microorganisms are pathogens of firs cultivated as Christmas trees. Among those, Phytophthora causes millions of dollars in damage to plantations annually. In Canada, it is still not known which species are responsible for Phytophthora root rot (PRR) of cultivated Abies species. Between 2019 and 2021, soil and root samples were collected from 40 Christmas tree plantations in Quebec province. We used soil baiting and direct root isolation to assess the diversity of culturable Phytophthora spp. The obtained isolates were identified with a multi-locus sequencing approach, and we used the sequencing data to place them along the Phytophthora phylogeny. A total of 44 isolates from six different Phytophthora species were identified, one fitting the provisional species P. sp.{square}kelmania{square}. A seventh taxa, represented by a group of 10 isolates, could not be assigned to any known Phytophthora species. Among the known species, Phytophthora abietivora was the most prevalent isolated species associated with PRR. Pathogenicity trials confirmed the pathogenicity potential of P. abietivora on both Fraser and balsam fir seedlings. Our studies provide a first snapshot of the Phytophthora diversity in Quebecs Christmas tree productions and describe multiple potential first associations between Phytophthora species and Abies balsamea and A. fraseri.

Soft rot Pectobacteriaceae (SRP) are among the most economically important plant pathogenic bacteria and are especially known to be problematic in potato production. The epidemiology of disease transmission has been investigated for almost a century, and several aspects have been highlighted as plausible infection routes. However, it is generally accepted that the major source of disease is the latently infected mother tuber, but several parameters are still influencing disease prevalence including contaminated equipment, soil water status as well as temperature. Management of the disease is limited to hygiene practices, dry storage and seed certification systems but several studies have also proven biocontrol agents such as bacteriophages (phages) as promising tools. Despite the severity of SRP on potato production, little is known about the genetic diversity of SRPs in Denmark, and since only few isolates are available, the possibility to design a broadly effective phage cocktail is limited. Here we describe a three-year field study utilizing an agri-citizen science approach where Danish farmers provided symptomatic potato plants or tubers, together with metadata such as date, location, potato variety and origin. By using whole genome sequencing (Illumina and Nanopore) together with metadata we were able to investigate and monitor the epidemiological disease spread across the country using 103 complete genomes, sampled across all three years. In this study we provide epidemiological evidence of disease origins and a suite of phages that could be used as a biocontrol tool for early disease intervention. Our results revealed several clonal clades across diverse locations (SNPs < 20) which strongly indicate common origin. A total of 17 Pectobacterium phages were tested and did target > 80% of clonal clades. Based on the clonality across the soft rot isolates we propose the possibility to set in early on using phages targeting strains relevant for soft rot development, with the possibility of a surveillance program together with customizing the phage preference.

Leptosphaeria maculans is one of the major fungal pathogens on oilseed rape (Brassica napus), causing stem canker disease. The closely related Brassica species Brassica nigra, Brassica juncea, and Brassica carinata display extreme resistance toward stem canker. In this study, we demonstrate the nonhost status of B. carinata toward L. maculans in France through field experiments and inoculations performed in controlled conditions. A few isolates moderately adapted to B. carinata, in controlled conditions, were recovered in the field on B. nigra leaves, allowing us to investigate the unusual B. carinata - L. maculans interactions using molecular, macroscopic, and microscopic analyses. A cross between a L. maculans isolate adapted to B. napus and an isolate moderately adapted to B. carinata allowed the generation, in the lab, of recombinant L. maculans strains better adapted to B. carinata than the natural parental isolate obtained from B. nigra, and highlighted the polygenic determinism of the adaptation of L. maculans to B. carinata and B. napus. This biological material will allow further investigation of the molecular determinants of the adaptation of L. maculans to nonhost species and elucidate the genetic resistance basis of B. carinata.

The continuous changes in the lineage proportions of populations in the clonal plant pathogen Phytophthora infestans on potato and tomato crops have been perplexing to researchers and disease managers. Sudden outbreaks of newly emergent genotypes are often associated with these rapid composition changes. Modelling can predict the persistence and displacement of pathogen genotypes with differential fitness among hosts. Building upon previous models, we combined analytical and simulation methods to model the outcome of interactions between competing lineages on multiple hosts. Model inputs include pathogenesis parameters, and the outputs are fitness and lineage proportions within each host. Analytical solutions yielding complete displacement, partial coexistence-displacement, and complete coexistence were described. In a retrospective study, the lesion growth rate and sporulation density of P. infestans lineages on potato and tomato from pathogenicity trials were used as inputs. Output lineage frequencies were compared with historical epidemiological situations to check model accuracy. The results showed that pathogenesis traits measured from empirical trials could simulate lineage constituents on potato and tomato, and estimate genotypic fitness with reasonable accuracy. The model also showed promise in predicting ongoing lineage displacements in the subsequent year or few years, even when the displaced lineage was still highly prevalent during the time of isolation. However, large uncertainties remain at temporal-spatial scales owing to complex meta-population dynamics in some regions and adaptation to local environmental factors. This simulation model provides a new tool for forecasting pathogen compositions, and can be used to identify potentially problematic genotypes based on pathogen life-history traits.

The obligate biotrophic fungus Blumeria graminis f. sp. tritici (Bgt) is the causal agent of wheat powdery mildew. To investigate virulence diversity, 30 Australian Bgt isolates collected between 2020 and 2024 were screened against a panel of 24 wheat lines carrying defined resistance (R) genes. Pathotyping analysis indicated that the Australian Bgt population is diverse in its virulence profile. Non-metric multidimensional scaling analysis of disease phenotyping revealed evidence of six distinct Bgt pathotype groups. In addition, we identified wheat varieties carrying defined R genes and their combinations that remain effective against the contemporary Australian Bgt. Notably, wheat cvs Khapli and Tabasco, possessing Pm4a and Pm2, respectively, in addition to unknown R gene(s), were highly resistant to all the isolates tested. Furthermore, elite European varieties that possess durable resistance, such as Alchemy and Cordiale, display complete to moderate resistance against all selected isolates representing the Australian pathotype groups.

Clubroot, caused by the obligate parasite Plasmodiophora brassicae, is one of the most devastating diseases affecting the canola/oilseed rape (Brassica napus) industry worldwide. Currently, the planting of clubroot-resistant (CR) cultivars is the most effective strategy used to restrict the spread and the economic losses linked to the disease. However, virulent P. brassicae isolates have been able to infect many of the currently available CR cultivars, and the options to manage the disease are becoming limited. Another challenge has been achieving consistency in evaluating host reactions to P. brassicae infection, with most bioassays conducted in soil and/or potting medium, which requires significant space and can be labour intensive. Visual scoring of clubroot symptom development can also be influenced by user bias. Here, we have developed a hydroponic bioassay using well-characterized P. brassicae single-spore isolates representative of clubroot virulence in Canada, as well as field isolates from three Canadian provinces, in combination with canola inbred homozygous lines carrying resistance genetics representative of CR cultivars available to growers in Canada. To improve the efficiency and consistency of disease assessment, symptom severity scores were compared with clubroot evaluations based on the scanned root area. According to the results, this bioassay offers a reliable, less expensive, and reproducible option to evaluate P. brassicae virulence, as well as a means to identify which canola resistance profile(s) may be effective against particular isolates. This bioassay will contribute to the breeding of new CR canola cultivars and the identification of virulence genes in P. brassicae that could trigger resistance and have been very elusive to this day.

Sporodochia are dense masses of fungal hyphae bearing asexual conidia. For Fusarium oxysporum, sporodochia are known to produce airborne conidia and enhance the dissemination of this otherwise soilborne pathogen. Sporodochia are small and transient, and they are documented for only a few formae speciales of Fusarium oxysporum. This study reports airborne conidia and sporodochia produced by F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry, in the Monterey Bay region of California. Sporodochia were consistently present in Fusarium wilt-afflicted strawberry fields and were discovered in 21 of 24 Fusarium wilt-diseased fields. Only necrotic tissues were observed bearing sporodochia, and they were most frequently observed on petioles and peduncles. Sporodochia grew significantly longer up peduncles than petioles, extending further away from the base of the plant and toward parts of the canopy more exposed to wind. A stolon hosted the longest stretch of sporodochial growth, found covering the stolons entire 35 cm length and also the base of the daughter plant. Macroconidia were produced by all sporodochia samples, and we did not find microconidia on any samples. An initial series of experiments confirmed the potential for conidia produced by sporodochia to disperse with wind over short distances. The prevalence of sporodochia producing airborne spores of F. oxysporum f. sp. fragariae has great importance for disease management and biosecurity.