Complete Genome Sequences of Six Copper-Resistant Xanthomonas Strains Causing Bacterial Spot of Solaneous Plants, Belonging to X. gardneri, X. euvesicatoria, and X. vesicatoria, Using Long-Read Technology

Xanthomonas vesicatoria, Xanthomonas euvesicatoria, and Xanthomonas gardneri cause bacterial spot disease. Copper has been applied since the 1920s as part of integrated management programs. The first copper-resistant strains were reported some decades later. Here, we fully sequenced six Xanthomonas strains pathogenic to tomato and/or pepper and having a copper-resistant phenotype.EEA Bella VistaFil: Richard, Damien. CIRAD, UMR PVBMT; Francia. ANSES, Plant Health Laboratory; Francia. Université de la Réunion; FranciaFil: Boyer, Claudine. CIRAD, UMR PVBMT; FranciaFil: Lefeuvre, Pierre. CIRAD, UMR PVBMT; FranciaFil: Canteros, Blanca Isabel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bella Vista; ArgentinaFil: Beni-Madhu, Shyam. FAREI; Isla MauricioFil: Portier, Perrine. Institut Nationale de la Recherche Agronomique. Institut de Recherche en Horticulture et Semences; FranciaFil: Pruvost, Olivier. CIRAD, UMR PVBMT; Franci

Sélection d'écotypes bactériens pathogènes et non-pathogènes par la plante en relation avec la différenciation en espèces génomiques chez Agrobacterium spp.

The aims of this work were : 1) to verify the existence of relations between genomic species and plant-associated ecotypes in Agrobacterium genus ; 2) to determine which genomic zones are implied in the ecotype differenciation and thus in the genomic species differenciation in this taxa. Firstly, we determined and caracterised, at the genomic level (by AFLP), non-pathogenic and pathogenic (harbouring a Ti plasmid) ecotypes in different biotopes. Our results show that the plant select specific ecotypes among the agrobacterial soil community. Moreover, some pathogenic strains, isolated from crown galls, are recruited among these particular ecotypes. Secondly, predictive AFLP performed on strain C58 genome, permitted us to identify the AFLP fragments caracteristic of genomic species G8. The genes and functions revealed this way could actually be implied in plant-bacteria relationships.Ce travail avait pour but : 1) de vérifier l'existence d'une relation entre espèces génomiques et écotypes associés aux plantes chez Agrobacterium spp.; 2) d'identifier les zones génomiques impliquées dans la différentiation en écotypes et, partant, en espèces génomiques dans ce taxon. Nous avons d'abord cherché et caractérisé au niveau génomique (par AFLP) des écotypes non-pathogènes et pathogènes (hébergeant un plasmide Ti), dans différents biotopes. Nos résultats montrent que la plante sélectionne des écotypes spécifiques au sein de la communauté des agrobactéries du sol. De plus, il apparaît que c'est parmis les écotypes spécifiques d'une plante donnée que sont recrutées certaines agrobactéries pathogènes isolées des tumeurs. L'AFLP prédictive réalisée sur le génome de la souche C58 nous a ensuite permis d'identifier les fragments AFLP caractéristiques de l'espèce G8. Les gènes et fonctions ainsi révèlées pourraient effectivement concerner des relations plantes-bactéries

Détermination d'un rythme de perfusion de romifidine pour induire une sédation chez le cheval (effet de l'adminitration concomittante de butorphanol)

LYON1-BU Santé (693882101) / SudocTOULOUSE-EN Vétérinaire (315552301) / SudocSudocFranceF

The CIRM in the new European landscape of biodiversity preservation: towards a deposition policy for INRA biological resources?

The Centre International de Ressources Microbiennes (CIRM) was created by INRA in 2004. The CIRM is now a network of five collections dedicated to the preservation, distribution and exploration of microbial biodiversity. It preserves more than 15,000 strains of plant, food and pathogenic bacteria, yeasts and filamentous fungi. CIRM is a Biological Research Center (BRC), ISO 9001 certified since 2008. The CIRM coordinated the European infrastructure project EMbaRC, which brought together 8 major microbial BRCs in Europe (www.embarc.eu). The CIRM is now partner of a larger infrastructure project established on the ESFRI roadmap, MIRRI (Microbial Resource Research Infrastructure). It includes over 70 microbial domain resource centers in 26 European countries (www.mirri.eu). Type strains are deposited in public collections under the pressure of journal editors and various international committees. However, despite the existence of dedicated BRCs, a very small proportion of published strains are deposited in such structures (1); this restricts further research and jeopardizes valorization of the biological material. To improve this situation, CIRM encourages strain deposit by INRA scientists. In return, CIRM ensures a high standard preservation and an enhanced visibility of the deposited material through its display in various databases (CIRM and FBRCMi databases, WFCC web site, StrainInfo.net…). In addition, CIRM also provides protection of the intellectual properties of the deposited material. Together with Inra scientists, CIRM therefore proposes to establish a deposition policy to improve the availability and visibility of INRA biological resources. This joint enterprise will constitute a strong example for the new landscape of European biodiversity preservation, which is currently being built in the MIRRI project

Pectobacterium aquaticum sp. nov., isolated from waterways

International audienceThis work aimed to establish the taxonomic status of six strains (A212-S19-A16T, A127-S21-F16, A105-S21-F16, A104-S21-F16, A101-S19-F16 and A35-S23-M15) isolated from three different waterways in 2015 and 2016 in south-east France. Amplification and sequencing of the gapA housekeeping gene clustered these six strains together inside the genus Pectobacterium outside of already described or proposed Pectobacterium species and supspecies. Phenotypic analysis, using GENIII Biolog plates performed with strains A212-S19-A16T, A105-S21-F16, A101-S19-F16 and the closely related Pectobacterium polaris (CFBP 1403), Pectobacterium carotovorum subsp. odoriferum (CFBP 1878T), ‘ Pectobacterium carotovorum subsp. actinidiae’ (CFBP 7370), Pectobacterium carotovorum subsp. carotovorum (CFBP 2046T), ‘ Pectobacterium carotovorum subsp. brasiliense ’ (CFBP 6617) or the most distantly related Pectobacterium aroidearum (CFBP 8168T) failed to identify specific compounds metabolized by these three strains, but weak activity was specifically observed at pH 5 with these three strains. Illumina sequencing was used to sequence these six strains. Based on phylogenetic data, average nucleotide identity values and in silico DNA–DNA hybridization results, strains A212-S19-A16T, A127-S21-F16, A105-S21-F16, A101-S19-F16, A35-S23-M15 and A104-S21-F16 are suggested to represent a novel species of the genus Pectobacterium , for which the name Pectobacterium aquaticum sp. nov. is proposed. The type strain is A212-S19-A16 T (=CFBP 8637T=NCPPB 4640T)

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

International audienceBacterial collections are invaluable tools for microbiologists. However, their practical useis compromised by imprecise taxonomical assignation of bacterial strains. This is particularly truefor soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp

Back to basics : Rethinking the diversity and pathogeny of the causal agent of Bacterial Leaf Spot of Lettuce

International audienc

Draft Genome Sequences of the Type Strains of Three Clavibacter Subspecies and Atypical Peach-Colored Strains Isolated from Tomato

Here, we present the draft genome sequences of 10 Clavibacter sp. strains, including the type strains of different subspecies of Clavibacter michiganensis and a potentially novel species within the genus. Genome lengths of the strains varied between 2,982,864 and 3,288,331 bp, with G+C contents of 72.23 to 73.50%