Plant Pathology

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.

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.

Tomatoes are an important crop worldwide and phytopathogens can cause devastating losses. Our study describes a treatment, consisting of Azospirillum brasilense Sp7 and either tomato seedling exudate or the exudate compound cytidine. The combination of A. brasilense Sp7 with cytidine showed a remarkable reduction of 83.4% in disease severity of tomatoes challenged with Pseudomonas syringae pv. tomato DC3000. Replacing cytidine with exudate was less effective at 71%, but the reduction in disease severity was still larger than by A. brasilense Sp7 alone at 55%. This reduction in disease severity was not paralleled by a decrease in P. syringae in leaf homogenates. Cytidine caused a 6.7 fold increase in A. brasilense Sp7 16S rDNA in root homogenates. In phyllosphere and rhizosphere, treatments modulated the microbial composition. In the phyllosphere, A. brasilense together with cytidine or tomato seedling exudate reduced the presence of eight human and/or plant pathogens in P. syringae challenged test groups. In the rhizosphere, principal component analysis revealed that variation along PC1 was dominated by the presence or absence of A. brasilense. Intriguingly, the inoculant caused an increase in the abundance of other Azospirillales species. Les tomates sont une culture dimportance mondiale, et les phytopathogenes peuvent entrainer des pertes devastatrices. Notre etude decrit un traitement compose dAzospirillum brasilense Sp7 et soit dun exsudat de plantules de tomate, soit de la cytidine, un compose particulier provenant des exsudats et suppose avoir un effet chimiotactique. Lassociation de A. brasilense Sp7 avec la cytidine a entraine une reduction remarquable de 83,4 % de la severite de la maladie parmi les plantes de tomate infectees par Pseudomonas syringae pv. tomato DC3000. Le remplacement de la cytidine par des exsudats etait moins efficace (71 %), bien que la reduction de la severite de la maladie ait demeure superieure a celle obtenue avec A. brasilense Sp7 seul (55 %). Cette diminution de la severite de la maladie na toutefois pas ete accompagnee dune reduction de la concentration de P. syringae dans les homogenats foliaires. La cytidine a provoque une augmentation de 6,7 fois de lADNr 16S de A. brasilense Sp7 dans les homogenats racinaires. Dans la phyllosphere et la rhizosphere, les traitements ont module la composition microbienne. Dans la phyllosphere, A. brasilense associe a la cytidine ou aux exsudats de plantules de tomate a reduit la presence de huit agents pathogenes humains et/ou vegetaux. Dans la rhizosphere, lobservation la plus remarquable est que la composante (PC1) de lanalyse en composantes principales (ACP) etait fortement influencee par la presence ou labsence de linoculum. De maniere interessante, A. brasilense Sp7 a entraine une augmentation de labondance dautres especes dAzospirillales.

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.

Esca and Black Dead Arm (EBDA) are complex grapevine trunk diseases (GTD) that are major causes of mortality and production decline in French vineyards. Unravelling the different factors that determine symptom expression is crucial in mitigating the impact on growers. While cultivar, climate, age, and pruning system are known contributors, they do not fully explain the variability in EBDA occurrence. This study investigates the role of grapevine vigour as a determinant factor in EBDA expression. In 2022 and 2023, three vineyard networks were monitored, each consisting of approximately 30 vineyard plots of Grenache Noir, uniform in age. To minimize climate variation the selected vineyards were located within small geographical areas. We evaluated grapevine vigour and its primary drivers--water and nitrogen status, weed cover, production, and vegetation biomass--and correlated these factors with EBDA occurrence. Results show that current-year vigour is positively correlated with the EBDA incidence rate in all network*year scenarios. The relationship curve suggests that, while low to moderate vigour is consistently associated with reduced symptom expression, high vigour can be correlated with either high or low expression and implies the involvement of additional factors. In one instance, previous year water stress, of all tested variables, was most correlated with current year EBDA incidence, though vigour was also influential. In that case, EBDA expression seems to be maximal when water stress the year before is combined with a substantial current year spring vigour. While these results need to be confirmed over a longer period, in more regions and with other cultivars, they open new perspectives of applications for growers. They suggest a wider implication of grapevine physiology than just vigour.

BackgroundPotato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress ("cry-for-help" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating members of the plant microbiota to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight. ResultsControlled foliar infection triggered substantial, cultivar-specific shifts in the rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were concerned by the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates. The inhibition potential of these strains against P. infestans spores was assessed through biological assays, which revealed the biocontrol potential of strains otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one. ConclusionTaken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains with efficient protective abilities against their host plants pathogens, which possibly contribute to its higher resistance against P. infestans.

Developing grapevine cultivars with genetic resistance to pathogens is a key strategy to reduce fungicide use and enhance sustainability. The French INRAE-ResDur program aims to pyramid several resistance loci against Plasmopara viticola (Rpv), the causal agent of downy mildew, while integrating factors against Erysiphe necator (Ren/Run) which causes powdery mildew. We evaluated in field the performance of grapevine genotypes carrying single or pyramided Rpv loci during the exceptionally severe downy mildew epidemic of 2024. Disease severity was quantified as the proportion of leaf foliage exhibiting symptoms. Susceptible controls averaged 66.6 % symptomatic leaves, Rpv1/3.1 combination remained below 16.1 %. whereas the Rpv1/Rpv3.1/Rpv10 pyramid showed only 4.9 % symptomatic leaves. The single loci provided partial protection, but the effect varied with genetic background. Pyramiding improved resistance effectiveness and stability, indicating synergistic interactions among loci. These findings demonstrate that pyramiding Rpv loci is an effective strategy for durable downy mildew resistance and should be the preferred strategy in grapevine breeding programs and genetic resistance deployment strategies.

The interplay between plant host, phytopathogenic bacteria, and enteric human pathogens in the phyllosphere have consequences for human health. Salmonella enterica has been known to take advantage of phytobacterial infection to increase its success on plants, but there is little knowledge of additional factors that may influence the relationship between enteric pathogen and plant disease. In this study, we investigated the role of humidity and the extent of plant disease progression on S. enterica colonization of plants. We found that high humidity was necessary for replication of S. enterica on diseased lettuce, but not required for S. enterica ingress into the UV-protected apoplast. Additionally, the Xanthomonas hortorum pv. vitians (hereafter, X. vitians) - infected lettuce host was found to be a relatively hostile environment for S. enterica when it arrived prior to the development of watersoaking or following necrosis onset, supporting the existence of an ideal window during X. vitians infection progress that maximizes S. enterica survival. In vitro growth studies in sucrose media suggest that X. vitians may allow S. enterica to benefit from cross-feeding during plant infection. Overall, this study emphasizes the role of phytobacterial disease as a driver of S. enterica success in the phyllosphere, demonstrates how time of arrival during disease progress can influence S. entericas fate in the apoplast, and highlights the potential for humidity to transform an infected apoplast into a growth-promoting environment for bacterial colonizers. ImportanceBacterial leaf spot of lettuce caused by X. vitians is a common threat to leafy green production. The global impact caused by phytopathogens, including X. vitians, is likely to increase with climate change. We found that even under a scenario where increased humidity did not enhance plant disease, high humidity had a substantial effect on facilitating S. enterica growth on Xanthomonas-infected plants. High humidity climates may directly contribute to the survival of human enteric pathogens in crop fields or indirectly affect bacterial survival via changes to the phyllosphere brought on by phytopathogen disease.

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.

Zymoseptoria tritici causes the most damaging wheat disease in Europe, septoria tritici blotch (STB). In Europe, STB is controlled mainly by fungicides and fungicide resistance is frequently reported. While fungicide resistance is thought to emerge mainly from standing genetic variation within field populations of Z. tritici, few studies have attempted to quantify the degree of fungicide resistance occurring at the field scale and to measure changes in frequencies of resistant strains following fungicide applications during a single growing season. Even fewer studies have considered the effects of different wheat cultivars on the emergence of fungicide resistance. We measured EC50 values for 1005 strains of Z. tritici sampled at two time points from 17 different wheat cultivars growing in a replicated field experiment that was treated with combinations of five different fungicides three times during the growing season. We found that field populations of Z. tritici can maintain a very high diversity in fungicide sensitivity phenotypes despite three fungicide treatments, with as much diversity found within a single field during a single growing season as has been described across all of Europe over several years. Multidrug resistance to two or more fungicides was found in 18.9% of the tested strains. We discovered that wheat cultivars that were more resistant to STB tended to be colonized by Z. tritici strains that exhibited higher fungicide resistance. We also found that specific wheat cultivars selected for resistance to specific active ingredients. Overall, our findings illustrate the many challenges associated with designing fungicide treatment programs that aim to reduce selection for fungicide resistance when confronted with a pathogen like Z. tritici that has a very high evolutionary potential.

AbstractGrapevine downy mildew, caused by Plasmopara viticola, is one of the most destructive diseases in viticulture. Resistance-based management strategies rely on grapevine varieties carrying major resistance loci (Rpv). Although breakdown of several loci has been reported, Rpv1 had remained effective until now. Here, we provide the first evidence of Rpv1 breakdown by P. viticola in Cilaos on Reunion Island (France) and the first case of a strain simultaneously overcoming three resistances of grapevine. We combined pathogenicity assays with whole-genome sequencing to characterize a P. viticola strain collected in Cilaos in 2023, alongside a panel of eight reference strains of known virulence. Hypersensitive response and sporulation were assessed for each strain on Chardonnay (susceptible variety) and four resistant varieties carrying Rpv1, Rpv3.1, Rpv10, or Rpv12. The strain collected in Cilaos was able to overcome not only Rpv1 but also Rpv3.1 and Rpv10. On Rpv1, we observed a complete loss of host recognition with high sporulation. On Rpv3.1, the phenotype was consistent with previous breakdowns, and the strain carried the vir1 allele previously described in France. By contrast, the breakdown of Rpv10 differed from that reported in European populations: whereas European strains displayed only partial breakdown of resistance, the strain of Cilaos showed complete loss of host recognition with high sporulation. Moreover, genomic analyses revealed a novel mutation, a large homozygous deletion in the corresponding avr locus. Our genomic data analyses further suggests that this P. viticola strain shares a genetic background with populations from mainland France, raising serious concerns about the potential emergence and spread of multivirulent lineages in Europe. These findings highlight the need for large-scale virulence monitoring of P. viticola and improved strategies for the sustainable management of grapevine resistance in Europe.

The number of small-scale diversified vegetable growers in industrialized countries has risen sharply over the last ten years. The risks associated with plant viruses in these systems have been barely studied in Europe, yet dramatic virus emergence events, such as tomato brown fruit rugose virus, sometimes occur. We developed a methodology that aimed to understand better the implications related to viruses for tomato production in Belgians vegetable farms by comparing growers perception of the presence of viral symptoms (visual inspection) with non targeting detection of nearly all viruses present in the plants by high throughput sequencing technologies (HTS). Virus presence and impact were interpreted considering the farms typology and cultural practices, the growers professional profiles, and visual inspection of plant-viral-like symptoms. Overall, The data indicated that most growers have limited understanding of tomato viruses and are not concerned about them. Field observations were correlated to this perception as the prevalence of symptomatic plants was usually lower than 1%. However, important and potentially emergent viruses, mainly transmitted by insects, were detected in several farms. Noteworthy, the presence of these viruses was correlated with the number of plant species grown per site (diversity) but not with a higher awareness of the growers regarding plant viral diseases or a higher number of symptomatic plants. In addition, both HTS and perception analysis underlined the rising incidence and importance of an emergent virus: Physostegia chlorotic mottle virus. Overall, the original methodology developed here, combining social science with HTS technologies, could be applied to other crops in other systems to identify emergent risks associated with plant viruses and can highlight the communication needed toward growers to mitigate epidemics.

Wheat blast, caused by Pyricularia oryzae Triticum (PoT), is an emergent threat to wheat production. Current understanding of the evolution and population biology of the pathogen and epidemiology of the disease has been based on phylogenomic studies that compared the wheat blast pathogen with isolates collected from grasses that were invasive to Brazilian wheat fields. Genetic similarity between isolates from wheat and grasses lead to the conclusion that significant cross-infection occurs, especially on signalgrass (Urochloa spp.); and this in turn prompted speculation that its widespread use as forage is a key driver of the diseases epidemiology. We reanalyzed data from those studies and found that all but one of the isolates from non-wheat hosts were members of PoT and the related Lolium-adapted lineage (PoL1), which meant that the Pyricularia populations typically found on endemic grasses had not yet been sampled. To address this shortcoming, we performed a comprehensive sampling of blast lesions in wheat crops and endemic grasses found in and away from wheat fields in Minas Gerais. A total 1,368 diseased samples were collected (976 leaves of wheat and grasses and 392 wheat heads) which yielded a working collection of 564 Pyricularia isolates. We show that, contrary to earlier implications, PoT was rarely found on endemic grasses and, conversely, members of grass-adapted populations were rarely found on wheat. Instead, most populations were host-specialized with constituent isolates usually grouping according to their host-of-origin. With regard to the dominant role proposed for signalgrass in wheat blast epidemiology, we found only one PoT member in 67 isolates collected from signalgrass grown away from wheat fields, and only three members of Urochloa-adapted populations among hundreds of isolates from wheat. Cross-inoculation assays on wheat and a signalgrass used in pastures (U. brizantha) suggested that the limited cross-infection observed in the field may be due to innate compatibility differences. Whether or not the observed level of cross-infection would be sufficient to provide an inoculum reservoir, or serve as a bridge between wheat growing regions, is questionable and, therefore, deserves further investigation.

O_LILeaf mould, caused by Fulvia fulva, is a devastating disease of tomato plants. In many commercial tomato cultivars, resistance to this disease is governed by the Cf-9 locus, which comprises five paralogous genes (Cf-9A-9E) that encode receptor-like proteins. Two of these proteins contribute to resistance: Cf-9C recognizes the previously identified F. fulva effector Avr9 and provides resistance during all plant growth stages, while Cf-9B recognises the yet-unidentified F. fulva effector Avr9B and provides mature plant resistance only. In recent years, F. fulva strains have emerged that have overcome the Cf-9 locus, with Cf-9C circumvented through Avr9 deletion. To understand how Cf-9B is circumvented, we set out to identify Avr9B. C_LIO_LIComparative genomics, in planta transient expression assays and gene complementation experiments were used to identify Avr9B, while gene sequencing was used to assess Avr9B allelic variation across a worldwide strain collection. C_LIO_LIA strict correlation between Avr9 deletion and resistance-breaking mutations in Avr9B was observed in strains recently collected from Cf-9 cultivars, whereas Avr9 deletion but no mutations in Avr9B were observed in older strains. C_LIO_LIThis research showcases how F. fulva has evolved to sequentially break down the two functional resistance genes of the complex Cf-9 locus and highlights that this locus now has limited value for controlling leaf mould disease in worldwide commercial tomato production. C_LI

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.

Phytophthora oleae is a pathogen recently reported to cause fruit rot on olive orchards in Italy and root rot in a natural wild-olive forest in Spain. RNAseq analysis was conducted to gain insight into the molecular mechanisms that trigger a plant defense response upon the inoculation of drupes with P. oleae and the pre- treatment with the antagonistic yeast Candida oleophila or with culture filtrates of the antagonistic filamentous fungus Trichoderma atroviride. Both treatments were applied to the olive drupe 24 h before the inoculation with the pathogen. Although no full resistance was observed, the virulence of P. oleae was reduced when the drupes were co-inoculated with the yeast or treated with culture filtrates of Trichoderma. Severity of Phytophthora rots in olive drupes was assessed at 24, 72, and 168 hours post pathogen inoculation (hpi) and rated based on an empirical scale. The most effective in reducing the disease severity of P. oleae infection on olive fruit was the treatment with T. atroviride filtrate (56% reduction), followed by C. oleophila (52%). Results showed that 2,466, 1,883, and 1,757 genes were differentially expressed in response to P. oleae, to the binary pathosystem C. oleophila and P. oleae, and T. atroviride and P. oleae, respectively, as compared to wound. Differential RNAseq by DESeq2, performed at 72 hours post-inoculation, and qPCR validation, at 24, 72, and 168 hpi, of the top differentially expressed genes defined a new pattern of plant defense mechanisms involving both PAMP and ETI immunity, with production of ROS and PRs.

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.

From sowing in late summer until harvest in following summer, oilseed rape can be infected by several fungi, which foliar symptoms (leaf spots) coexist on the crop. Training an expert at their identification is quick for the typical symptoms with characteristic appearance. However, in many cases the size, colour and morphology are similar and for the atypical symptoms, there is a risk of confusion or in-decidability. Also, scouting the fields for expert training is not possible at all seasons and all diseases might not be seen in all years and all places. The aim of our study was to produce large sets of pictures annotated by several experts, from which tables illustrating the diversity of symptom appearance were chosen. These tables will enable assistance to diagnostic and expert training.

Wild potatoes are long-evolving relatives of the cultivated potatoes we have today. These wild Solanum species harbor traits that can be exploited to develop more nutritive and resilient potato varieties, providing the genetic basis for resistance to abiotic and biotic stresses such as drought, low temperatures, diseases and pests. Wild potato species are widely used as valuable genetic resources in breeding programs, including efforts aimed at improving resistance to bacterial wilt caused by Ralstonia solanacearum. Among the wild species native to Uruguay, Solanum malmeanum has emerged as a particularly valuable source of resistance. The aim of this work was to investigate weather differences in bacterial wilt resistance among S. malmeanum accessions are associated with structural and compositional changes of rhizosphere bacterial communities. Two S. malmeanum accessions were compared, one susceptible (RN9P2) and the other resistant (A11P1) to bacterial wilt. The impact of plant resistance and pathogen colonization on the structure of rhizosphere bacterial communities were evaluated using high throughput 16S rRNA gene amplicon-sequencing. Significant differences were observed between accessions and pronounced shifts in rhizosphere bacterial communities were detected in response to pathogen inoculation. Cryseobacterium, Sphingobacterium, Komagataeibacter, Gluconobacter, Lactobacillus and Dyella were differential genera and enriched in the rhizosphere of the resistant accession. Several of these genera have been previously associated with disease suppression. Overall, these results suggest that the rhizosphere bacterial community associated with resistant S. malmeanum accessions may contribute to protection against R. solanacearum infection.

Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases of grapevine worldwide. Primary inoculum (i.e. oospores) play a decisive role in downy mildew epidemics, but we still know very little about its abundance in vineyard soil. This study presents a novel molecular method for quantifying P. viticola oospore concentration in vineyard soil using digital droplet PCR (ddPCR). The development of this method enabled characterization of both the abundance and spatial distribution of oospores in a vineyard at the onset of the growing season. Following a regular grid, a total of 198 soil samples (0-15cm horizon) were collected in March 2022 in grapevine rows in a 0.22 ha vineyard planted with cv. Merlot and conducted according to French organic viticulture specifications. Additional samples were collected from the same field within five nested sampling plots with three distance levels, including samples collected in the inter-rows. Using ddPCR, we found P. viticola DNA in all soil samples except one, and we estimated that oospore concentration ranged from 0 to 1858 oospores per gram of soil (303 {+/-} 308 on average). The distribution of oospores at field scale was not random but characterized by 15 m-diameter patches of concentrically increasing oospore concentration. Oospores accumulated 5 times more below the vine stocks than in the inter-row. Using a leaf disc bioassay, we found that soil infectious potential significantly increased with oospore concentration assessed by ddPCR. However, the low coefficient of determination of the relationship indicated that DNA-based oospore quantification lacked clear epidemiological significance. Both ddPCR and bioassay methods are valuable tools that could be used to assess reservoirs of P. viticola primary inoculum across different agroclimatic contexts, thereby bringing greater genericity. Further methodological improvement will also help refine the accuracy of DNA-based assessment of primary inoculum reservoir and improve our understanding of the relationship between primary inoculum reservoir and epidemic dynamics. Ultimately, these data will be essential for improving epidemic risk models and evaluating new preventive disease management strategies targeting the primary inoculum. ImportanceGrapevine downy mildew caused by the oomycete Plasmopara viticola, affects leaves and bunches, and leads to important economic losses for viticulturists. Recently, evidences have accumulated that soilborne primary inoculum (i.e. oospores in the soil) importantly contributes to disease progress. The significance of our work is in presenting a direct and sensitive method for assessing soil oospore concentration, as well as quantitative and spatially-explicit data on downy mildew primary inoculum. This opens the way to new research, the evaluation of new disease control strategies based on primary inoculum management and the improvement of epidemic risk models, which will potentially contribute to lower fungicide use in viticulture in fine.