Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France.

Botryosphaeriaceae species are the major causal agents of walnut dieback worldwide, along with Diaporthe species. Botryosphaeria dothidea and Neofusicoccum parvum are the only two Botryosphaeriaceae species associated with this recently emergent disease in France, and little is known about their diversity, structure, origin and dispersion in French walnut orchards. A total of 381 isolates of both species were genetically typed using a sequence-based microsatellite genotyping (SSR-seq) method. This analysis revealed a low genetic diversity and a high clonality of these populations, in agreement with their clonal mode of reproduction. The genetic similarity among populations, regardless of the tissue type and the presence of symptoms, supports the hypothesis that these pathogens can move between fruits and twigs and display latent pathogen lifestyles. Contrasting genetic patterns between N. parvum populations from Californian and Spanish walnut orchards and the French ones suggested no conclusive evidence for pathogen transmission from infected materials. The high genetic similarity with French vineyards populations suggested instead putative transmission between these hosts, which was also observed with B. dothidea populations. Overall, this study provides critical insight into the epidemiology of two important pathogens involved in the emerging dieback of French walnut orchards, including their distribution, potential to mate, putative origin and disease pathways

Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

Background: Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi. Results: We sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc. Conclusions: This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Conditions d'expression de l'activité antagoniste de Pythium oligandrum Drechs., exercée seule ou en association avec d'autres micro-organismes, au sein de la rhizosphère de plants de tomate (lycopersicon esculentum Mill.)

P. oligandrum est un champignon mycoparasite de nombreux agents pathogènes racinaires et présente un fort potentiel comme agent de lutte biologique en culture hors-sol. L'étude des intéractions dans la rhizosphère, déclenchées par l'introduction de ce champignon nécessite pourtant des éclaircissements. Ainsi, le suivi de la colonisation racinaire par P. oligandrum à également permis une étude de l'implantation de la famille des Pythiacées en culture hors-sol. Les compétitions entre les organismes dans la rhizosphère ne semblent pas des mécanismes déterminants, mais l'induction de résistance systémique semble prévaloir et serait mieux à même d'expliquer le gain de rendement observé dans certaines conditions culturales. En outre, la rapidité et l'étendue de la colonisation par P. oligandrum corrélé à la rapidité de déclenchement des réponses de la plante met en évidence une interaction atypique entre un agent antagonsite et la plante.P. oligandrum is a mycoparasite of many roots pathogens and has a promising potential as a biocontrol agent in soilless culture. Study of the interactions in the rhizosphère, due to the introduction of this fungus however requires explanations. Thus, the evaluation of root colonization by P. oligandrum also allowed a study of the establishment of the Pythium spp. in soilless culture. Micro-organisms competitions in the rhizosphère don't seem determining mechanisms, but the systemic induction of resistance seems to prevail and could explain the yield improvement observed under farming conditions. Moreover, the speed and the extent of colonization by P. oligandrum correlated with the speed of release of the answers of the plant highlight an atypical interaction between an antagonistic agent and the plant.BREST-BU Droit-Sciences-Sports (290192103) / SudocSudocFranceF

L'unité biologique du bulbe d'Echalote au cours du temps

National audienc

Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities

International audienceFusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances

Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen–one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms

Enhancement of development and induction of resistance in tomato plants by the antagonist, Pythium oligandrum

To exert an optimal biological control, P. oligandrum must colonise roots and persist in the rhizosphere of plants throughout the cultural season. The present study demonstrated that, after inoculation of root system by P. oligandrum, it colonised 20 to 40% of roots of tomato plants grown in hydroponic system. Constant presence of the introduced fungus in the rhizosphere over the cultural season is correlated with an increase in tomato yield. The combination of several factors likely explains this P. oligandrum-mediated increase. Among them, one may cite mycoparasitism; however, though P. oligandrum can parasitize other pathogenic Pythium species; root colonisation by the antagonist was not associated with significant reduction in Pythium spp. populations. In the present case, the induction of plant resistance seems more prevalent. Indeed, root colonisation with P. oligandrum induced systemic resistance. Interestingly, P. oligandrum-inoculated plants triggered and amplified PR proteins synthesis only when leaves had been attacked by the pathogen, Botrytis cinerea.Augmentation du développement et induction de résistance chez des plants de tomate par l'agent antagoniste, Pythium oligandrum. Pour que Pythium oligandrum exerce un contrôle biologique optimal, il doit coloniser et persister dans la rhizosphère des plantes durant toute la saison culturale. La présente étude montre qu'après inoculation du système racinaire par Pythium oligandrum, celui-ci colonise 20 à 40 % des racines de plants de tomate cultivés dans un système hydroponique. La présence constante du champignon dans la rhizosphère tout au long de la saison culturale est corrélée avec une augmentation de rendement en tomates. La combinaison de plusieurs facteurs explique certainement l'augmentation induite par P. oligandrum. Parmi ceux-ci, on peut citer le mycoparasitisme. Bien que P. oligandrum puisse mycoparasiter d'autres espèces de Pythium pathogènes, la colonisation racinaire par l'antagoniste n'est pas associée avec une réduction significative des populations de Pythium spp. Dans le cas présent, l'induction de résistance chez la plante semble prévaloir. En effet, la colonisation des racines par P. oligandrum induit une résistance systémique. D'une façon remarquable, les plantes inoculées par P. oligandrum déclenchent et amplifient la synthèse de protéines PR seulement quand les feuilles sont attaquées par l'agent pathogène, Botrytis cinerea

Influence of Pythium oligandrum Biocontrol on Fungal and Oomycete Population Dynamics in the Rhizosphere▿

Fungal and oomycete populations and their dynamics were investigated following the introduction of the biocontrol agent Pythium oligandrum into the rhizosphere of tomato plants grown in soilless culture. Three strains of P. oligandrum were selected on the basis of their ability to form oospores (resting structures) and to produce tryptamine (an auxin-like compound) and oligandrin (a glycoprotein elicitor). Real-time PCR and plate counting demonstrated the persistence of large amounts of the antagonistic oomycete in the rhizosphere throughout the cropping season (April to September). Inter-simple-sequence-repeat analysis of the P. oligandrum strains collected from root samples at the end of the cropping season showed that among the three strains used for inoculation, the one producing the smallest amount of oospores was detected at 90%. Single-strand conformational polymorphism analysis revealed increases in the number of members and the complexity of the fungal community over time. There were no significant differences between the microbial ecosystems inoculated with P. oligandrum and those that were not treated, except for a reduction of Pythium dissotocum (ubiquitous tomato root minor pathogen) populations in inoculated systems during the last 3 months of culture. These findings raise interesting issues concerning the use of P. oligandrum strains producing elicitor and auxin molecules for plant protection and the development of biocontrol