Author: "Céline Lavire" - Searchworks@Jio Institute Digital Library Search Results

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35 results on '"Céline Lavire"'

1. Biochemical and molecular identification of a native Bacillus thuringiensis gv. cytolyticus isolate with insecticidal effect against the pod borer larvae (Helicoverpa armigera)

Author: Thameur Bouslama, Asma Laarif, Mayssa Chattaoui, Ludovic Vial, Céline Lavire, Jeanne Doré, and Ali Rhouma
Subjects: bacillus thuringiensis gv. cytolyticus, biological control, biolog, entomopathogenic bacteria, helicoverpa armigera, multi-locus sequence analysis, 16s rrna sequencing, Plant culture, SB1-1110, Plant ecology, QK900-989
Abstract: Bouslama, T., Laarif, A., Chattaoui, M., Vial, L., Lavire, C., and Doré, J., and Rhouma, A. 2023. Biochemical and molecular identification of a native Bacillus thuringiensis gv. cytolyticus isolate with insecticidal effect against the pod borer larvae (Helicoverpa armigera). Tunisian Journal of Plant Protection 18 (2): 71-91.
Published: 2023

2. Biological Control of Grapevine Crown Gall Disease, Caused by Allorhizobium vitis, Using Paraburkholderia phytofirmans PsJN

Author: Nguyen-Huu Trong, Jeanne Doré, Matthieu Gaucher, Cédric Jacquard, Nicolas Richet, Vincent Leclère, Essaïd Aït Barka, Marie Noëlle Brisset, Isabelle Kerzaon, Céline Lavire, Christophe Clément, Ludovic Vial, and Lisa Sanchez
Subjects: Agrobacterium/Allorhizobium vitis, biocontrol, crown gall disease, grapevine, opine, Paraburkholderia phytofirmans PsJN, Plant culture, SB1-1110, Botany, QK1-989
Abstract: Controlling crown gall in grapevine (Vitis vinifera L.) caused by the pathogenic bacterium Allorhizobium vitis is a major challenge for global viticulture, as this pathogen is highly persistent in vineyards once infected. The bacteria can enter the plant through open wounds during pruning and then systemically colonize the plant. This study aimed at evaluating the potential of Paraburkholderia phytofirmans PsJN, a beneficial endophytic bacterium able to colonize the xylem of grapevine, the same ecological niche as A. vitis, to control grapevine crown gall disease. P. phytofirmans PsJN was root-inoculated on grapevine plantlets before infection by A. vitis S4 on shoots. A. vitis S4 level in planta, vitopine production, accumulation of lignin in tumors, and symptoms of crown gall were investigated on grapevine prebacterized or not with PsJN. The expression of 28 grapevine genes involved in defense mechanisms was also simultaneously determined by quantitative real-time PCR. Despite a direct antibacterial effect against AvS4, PsJN has no significant impact on the incidence of crown gall or disease severity. However, PsJN leads to a stronger accumulation of vitopine in tumors and significantly reduced the population level of the pathogen in planta. [Figure: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Published: 2022
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3. Paraburkholderia phytofirmans PsJN delays Botrytis cinerea development on grapevine inflorescences

Author: Lidiane Carla Miotto Vilanova, Marine Rondeau, Mathilde Robineau, Jean François Guise, Céline Lavire, Ludovic Vial, Florence Fontaine, Christophe Clément, Cédric Jacquard, Qassim Esmaeel, Essaïd Aït Barka, and Lisa Sanchez
Subjects: Botrytis cinerea, protection, grapevine inflorescences, antigerminative effect, Paraburkholderia phytofirmans PsJN, Microbiology, QR1-502
Abstract: Grapevine flowering is an important stage in the epidemiology of Botrytis cinerea, the causal agent of gray mold disease. To prevent infection and to minimize postharvest losses, the control of this necrotrophic fungus is mainly based on chemical fungicides application. However, there is a growing interest in other control alternatives. Among them, the use of beneficial microorganisms appears as an eco-friendly strategy. This study aims to investigate the effect of Paraburkholderia phytofirmans PsJN, root-inoculated or directly sprayed on fruiting cuttings inflorescences to control B. cinerea growth. For this purpose, quantification by real time PCR of Botrytis development, direct effect of PsJN on fungal spore germination and chemotaxis were assayed. Our results showed a significant protective effect of PsJN only by direct spraying on inflorescences. Moreover, we demonstrated an inhibition exerted by PsJN on Botrytis spore germination, effective when there was a direct contact between the two microorganisms. This study showed that PsJN is positively attracted by the pathogenic fungus B. cinerea and forms a biofilm around the fungal hyphae in liquid co-culture. Finally, microscopic observations on fruit cuttings revealed a co-localization of both beneficial and pathogenic microorganisms on grapevine receptacle and stigma that might be correlated with the protective effect induced by PsJN against B. cinerea via a direct antimicrobial effect. Taking together, our findings allowed us to propose PsJN as a biofungicide to control grapevine gray mold disease.
Published: 2022
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4. Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

Author: Nitin K. Singh, Céline Lavire, Joseph Nesme, Ludovic Vial, Xavier Nesme, Christopher E. Mason, Florent Lassalle, and Kasthuri Venkateswaran
Subjects: Agrobacterium tomkonis, genomovar G3, ISS, metagenomics, phylogenomics, MLSA, Microbiology, QR1-502
Abstract: Strains of Agrobacterium genomospecies 3 (i.e., genomovar G3 of the Agrobacterium tumefaciens species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of Agrobacterium G3 strains to other Agrobacterium spp., which supports the description of a novel species. The G3 strains tested (n = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus Agrobacterium. Phylogenetic analyses of the 16S rRNA gene, gyrB gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the Agrobacterium genus and they form a clade distinct from other validly described Agrobacterium species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and in silico digital DNA–DNA hybridization (dDDH) comparisons between the G3 tested strains and all known Agrobacterium species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were Agrobacterium sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of Agrobacterium G3, showing it is a bona fide bacterial species, well separated from previously named Agrobacterium species or other recognized genomic species. We thus propose the name Agrobacterium tomkonis for this species previously referred to as Agrobacterium genomospecies 3. The type strain of A. tomkonis is IIF1SW-B1T (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show A. tomkonis strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. A. tomkonis specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The A. tomkonis strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.
Published: 2021
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5. Ecological Conditions and Molecular Determinants Involved in Agrobacterium Lifestyle in Tumors

Author: Thibault Meyer, Clémence Thiour-Mauprivez, Florence Wisniewski-Dyé, Isabelle Kerzaon, Gilles Comte, Ludovic Vial, and Céline Lavire
Subjects: Agrobacterium tumefaciens, tumor lifestyle, crown gall, molecular traits, competition, plant defense, Plant culture, SB1-1110
Abstract: The study of pathogenic agents in their natural niches allows for a better understanding of disease persistence and dissemination. Bacteria belonging to the Agrobacterium genus are soil-borne and can colonize the rhizosphere. These bacteria are also well known as phytopathogens as they can cause tumors (crown gall disease) by transferring a DNA region (T-DNA) into a wide range of plants. Most reviews on Agrobacterium are focused on virulence determinants, T-DNA integration, bacterial and plant factors influencing the efficiency of genetic transformation. Recent research papers have focused on the plant tumor environment on the one hand, and genetic traits potentially involved in bacterium-plant interactions on the other hand. The present review gathers current knowledge about the special conditions encountered in the tumor environment along with the Agrobacterium genetic determinants putatively involved in bacterial persistence inside a tumor. By integrating recent metabolomic and transcriptomic studies, we describe how tumors develop and how Agrobacterium can maintain itself in this nutrient-rich but stressful and competitive environment.
Published: 2019
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6. A simple and stable method of tagging Agrobacterium fabrum C58 for environmental monitoring

Author: Meriam BOURI, Haifa Ben GHARSA, Ludovic VIAL, Céline LAVIRE, Bernard R. GLICK, and Ali RHOUMA
Subjects: crown gall, gentamicin resistant cassette, chromosome, non-coding region, Botany, QK1-989
Abstract: Agrobacterium fabrum is one of the eleven Agrobacterium spp. complex species that has been observed to carry a Ti plasmid and induce crown gall, a disease causing significant damage to economically important perennial agricultural crops. Members of this species complex, including A. fabrum, are morphologically indistinguishable from one another on culture media and are known to grow together in soil and within host galls. Consequently, the tracking of this species in its natural environment requires a cautious approach to tagging strains without altering any of their ecologically important traits. A gentamicin resistant cassette (aacC1) was inserted, by homologous recombination, into a non-coding region of the A. fabrum C58 chromosome between the genes atu1182 and atu1183. The resultant strain did not show any significant in vitro growth differences compared to the wild-type strain, and the marker was stable in rich medium, both with and without selective pressure. The mutant/marked strain was indistinguishable from the parental strain for ability to induce galls, grow in bulk soil and colonize the rhizosphere of tomato plants. Easy, precise, safe and stable tagging of the A. fabrum C58 genome facilitates environmental population surveys by either simple selection or direct detection by PCR. This methodology provides understanding of the ecology of this species complex as an integral part of managing the soil microbiota for improved crown gall management.
Published: 2017
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7. Impact of Paraburkholderia phytofirmans PsJN on Grapevine Phenolic Metabolism

Author: Lidiane Miotto-Vilanova, Barbara Courteaux, Rosa Padilla, Fanja Rabenoelina, Cédric Jacquard, Christophe Clément, Gilles Comte, Céline Lavire, Essaïd Ait Barka, Isabelle Kerzaon, and Lisa Sanchez
Subjects: vitis vinifera, beneficial bacterium, phenolic compounds, qrt-pcr, uhplc-uv/dad-ms qtof, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract: Phenolic compounds are implied in plant-microorganisms interaction and may be induced in response to plant growth-promoting rhizobacteria (PGPRs). Among PGPR, the beneficial bacterium Paraburkholderia phytofirmans PsJN was previously described to stimulate the growth of plants and to induce a better adaptation to both abiotic and biotic stresses. This study aimed to investigate the impact of PsJN on grapevine secondary metabolism. For this purpose, gene expression (qRT-PCR) and profiling of plant secondary metabolites (UHPLC-UV/DAD-MS QTOF) from both grapevine root and leaves were compared between non-bacterized and PsJN-bacterized grapevine plantlets. Our results showed that PsJN induced locally (roots) and systemically (leaves) an overexpression of PAL and STS and specifically in leaves the overexpression of all the genes implied in phenylpropanoid and flavonoid pathways. Moreover, the metabolomic approach revealed that relative amounts of 32 and 17 compounds in roots and leaves, respectively, were significantly modified by PsJN. Once identified to be accumulated in response to PsJN by the metabolomic approach, antifungal properties of purified molecules were validated in vitro for their antifungal effect on Botrytis cinerea spore germination. Taking together, our findings on the impact of PsJN on phenolic metabolism allowed us to identify a supplementary biocontrol mechanism developed by this PGPR to induce plant resistance against pathogens.
Published: 2019
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8. Two Novel Species Isolated from Wheat Rhizospheres in Serbia: Pseudomonas Serbiensis Sp. Nov. And Pseudomonas Serboccidentalis Sp. Nov

Author: Irena Todorović, Danis Abrouk, Martina Kyselková, Céline Lavire, Marjolaine Rey, Vera Raičević, Jelena Jovičić-Petrović, Yvan Moënne-Loccoz, and Daniel Muller
Published: 2023

9. Development and validation of a UHPLC-ESI-QTOF mass spectrometry method to analyze opines, plant biomarkers of crown gall or hairy root diseases

Author: Isabelle Kerzaon, Yves Dessaux, David Chapulliot, Rosa Padilla, Floriant Bellvert, Xavier Nesme, Vincent Gaillard, Ludovic Vial, Thao Nhi Le, Céline Lavire, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Orléans (UO), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), French national program EC2CO (project IBAD) BioEnviS Research Federation French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche Consejo Nacional de Ciencia y Tecnologia (CONACyT)CVU 397515Rhone-Alpes international cooperation and mobility program (CMIRA), Institut de Chimie Organique et Analytique (ICOA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and CCSD, Accord Elsevier
Subjects: Spectrometry, Mass, Electrospray Ionization, Opines, Agrobacterium, Clinical Biochemistry, Opine, Arginine, Mass spectrometry, Plant Roots, 030226 pharmacology & pharmacy, 01 natural sciences, Biochemistry, Analytical Chemistry, Matrix (chemical analysis), 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Plant Tumors, Quantification, Diagnosis, Gall, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Mannitol, Chromatography, High Pressure Liquid, Plant Diseases, Octopine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Chromatography, biology, 010401 analytical chemistry, Crown (botany), Reproducibility of Results, food and beverages, Cell Biology, General Medicine, biology.organism_classification, 0104 chemical sciences, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Detection, chemistry, UHPLC-ESI-MS-QTOF, Nopaline, Biomarkers
Abstract: International audience; Opines are low-molecular-weight metabolites specifically biosynthesized by agrobacteria-transformed plant cells when plants are struck by crown gall and hairy root diseases, which cause uncontrolled tissue overgrowth. Transferred DNA is sustainably incorporated into the genomes of the transformed plant cells, so that opines constitute a persistent biomarker of plant infection by pathogenic agrobacteria and can be targeted for crown gall/hairy root disease diagnosis. We developed a general, rapid, specific and sensitive analytical method for overall opine detection using ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-MS-QTOF), with easy preparation of samples. Based on MS, MS/MS and chromatography data, the detection selectivity of a wide range of standard opines was validated in pure solution and in different plant extracts. The method was successfully used to detect different structural types of opines, including opines for which standard compounds are unavailable, in tumors or hairy roots induced by pathogenic strains. As the method can detect a wide range of opines in a single run, it represents a powerful tool for plant gall analysis and crown gall/hairy root disease diagnosis. Using an appropriate dilution of plant extract and a matrix-based calibration curve, the quantification ability of the method was validated for three opines belonging to different families (nopaline, octopine, mannopine), which were accurately quantified in plant tissue extracts.
Published: 2021

10. Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum

Author: Armelle Vigouroux, Anaïs Naretto, Pierre Legrand, Aurélie Di Cicco, Ludovic Vial, Daniel Lévy, Sébastien Renoud, Céline Lavire, Jeanne Doré, Magali Aumont-Nicaise, Solange Moréra, Thibault Meyer, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Synchroton Soleil, Division Experience/Ligne Nanoscopium, L'Orme des Merisiers, Gif-sur-Yvette, ANR-10-INSB-05-01 INSB ANR-10-INSB-0501, Universite de LyonED341-E2M2French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la RechercheFrench National Research Infrastructure France BioImagingANR10-INBS-04Centre National de la Recherche Scientifique (CNRS)European Commission, Synchrotron SOLEIL (SSOLEIL), Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Mesures d'interactions protéine-protéine (PIM), Département Plateforme (PF I2BC), Centre de recherche de l'Institut Curie [Paris], and Institut Curie [Paris]
Subjects: Models, Molecular, Coumaric Acids, Protein Conformation, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Allosteric regulation, Repressor, Agrobacterium, Biology, Crystallography, X-Ray, Sodium Citrate, 03 medical and health sciences, Allosteric Regulation, Bacterial Proteins, Protein Domains, Transcription (biology), Structural Biology, Genetics, Transcriptional regulation, Genes, Synthetic, Binding site, Promoter Regions, Genetic, Transcription factor, Tetrahydrofolates, 030304 developmental biology, 0303 health sciences, Binding Sites, Effector, 030302 biochemistry & molecular biology, Gene Expression Regulation, Bacterial, DNA binding site, Repressor Proteins, Zinc, Biochemistry, Multigene Family, Protein Multimerization
Abstract: A species-specific region, denoted SpG8-1b allowing hydroxycinnamic acids (HCAs) degradation is important for the transition between the two lifestyles (rhizospheric versus pathogenic) of the plant pathogen Agrobacterium fabrum. Indeed, HCAs can be either used as trophic resources and/or as induced-virulence molecules. The SpG8-1b region is regulated by two transcriptional regulators, namely, HcaR (Atu1422) and Atu1419. In contrast to HcaR, Atu1419 remains so far uncharacterized. The high-resolution crystal structures of two fortuitous citrate complexes, two DNA complexes and the apoform revealed that the tetrameric Atu1419 transcriptional regulator belongs to the VanR group of Pfam PF07729 subfamily of the large GntR superfamily. Until now, GntR regulators were described as dimers. Here, we showed that Atu1419 represses three genes of the HCAs catabolic pathway. We characterized both the effector and DNA binding sites and identified key nucleotides in the target palindrome. From promoter activity measurement using defective gene mutants, structural analysis and gel-shift assays, we propose N5,N10-methylenetetrahydrofolate as the effector molecule, which is not a direct product/substrate of the HCA degradation pathway. The Zn2+ ion present in the effector domain has both a structural and regulatory role. Overall, our work shed light on the allosteric mechanism of transcription employed by this GntR repressor.
Published: 2020

11. Development of a DNA-Based Real-Time PCR Assay To Quantify

Author: Trong, Nguyen-Huu, Jeanne, Doré, Essaïd, Aït Barka, Céline, Lavire, Christophe, Clément, Ludovic, Vial, and Lisa, Sanchez
Subjects: Agrobacterium, Vitis, DNA, Real-Time Polymerase Chain Reaction
Published: 2020

12. Clarifying the taxonomy of the causal agent of bacterial leaf spot of lettuce through a polyphasic approach reveals that Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym of Xanthomonas hortorum Vauterin et al. 1995

Author: Perrine Portier, Xavier Nesme, Marion Fischer-Le Saux, Céline Lavire, Emma R. Rosenthal, Franck Bertolla, Alexandre Burlet, Lucas Morinière, Carolee T. Bull, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station expérimentale Rhône-Alpes et Information Légumière, SERAIL, Department of Plant pathology and Environmental Microbiology, Pennsylvania State University (Penn State), Penn State System-Penn State System, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), L. Morinière was funded by a grant from the French Ministry ofHigher Education, Research and Innovation. The Rhône Alpes rural development program and funded bythe Rhône-Alpes region and FEADER program from the EU, and USDA National Institute of Food and Federal Appropriations and the California Leafy Greens Research Program and the California Department of Food and Agriculture.
Subjects: DNA, Bacterial, Xanthomonas, Pathovar vitians, Xanthomonas hortorum, Xanthomonas cynarae, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Terminology as Topic, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Leaf spot, Phylogenomic, Overall genome relatedness indices, Bacterial leaf spot of lettuce, Phylogeny, Ecology, Evolution, Behavior and Systematics, Plant Diseases, 030304 developmental biology, 0303 health sciences, Genes, Essential, biology, 030306 microbiology, Nucleic Acid Hybridization, Sequence Analysis, DNA, Lettuce, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Xanthomonas campestris, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Phenotype, Taxonomy (biology), Genome, Bacterial
Abstract: International audience; Assessment of the taxonomy and diversity of Xanthomonas strains causing bacterial leaf spot of lettuce(BLSL), commonly referred to as Xanthomonas campestris pv. vitians, has been a long-lasting issue whichheld back the global efforts made to understand this pathogen. In order to provide a sound basis essentialto its study, we conducted a polyphasic approach on strains obtained through sampling campaigns oracquired from collections. Results of a multilocus sequence analysis crossed with phenotypic assaysrevealed that the pathotype strain does not match the description of the nomenspecies provided byBrown in 1918. However, strain LMG 938 = CFBP 8686 does fit this description. Therefore, we proposethat it replaces LMG 937 = CFBP 2538 as pathotype strain of X. campestris pv. vitians.Then, whole-genome based phylogenies and overall genome relatedness indices calculated on taxo-nomically relevant strains exhibited the intermediate position of X. campestris pv. vitians between closelyrelated species Xanthomonas hortorum and Xanthomonas cynarae. Phenotypic profiles characterized usingBiolog microplates did not reveal stable diagnostic traits legitimizing their distinction. Therefore, we pro-pose that X. cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym ofX. hortorum, to reclassify X. campestris pv. vitians as X. hortorum pv. vitians comb. nov. and to transferX. cynarae pathovars in X. hortorum as X. hortorum pv. cynarae comb. nov. and X. hortorum pv. gardnericomb. nov. An emended description of X. hortorum is provided, making this extended species a promisingmodel for the study of Xanthomonas quick adaptation to different hosts
Published: 2020

13. Characterization and phylogenetic diversity of Allorhizobium vitis isolated from grapevine in Morocco

Author: Florence Wisniewski-Dyé, Khaoula Habbadi, El Hassan Achbani, Isabelle Kerzaon, Quentin Duplay, David Chapulliot, Rachid Benkirane, Abdellatif Benbouazza, Céline Lavire, Ludovic Vial, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculté des Sciences - Laboratoire de Biotechnologies Biochimie Valorisation et Protection des Plantes, Université Cadi Ayyad [Marrakech] (UCA), project 'Biological control against Agrobacterium vitis agent causal of Crown gall of grapevine' PRAD 14-08Regional Center of the National Institute for Agricultural Research Meknes (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: Agrobacterium, Glutamine, [SDV]Life Sciences [q-bio], Opine, Arginine, Applied Microbiology and Biotechnology, 03 medical and health sciences, Bacterial Proteins, Plant Tumors, Gall, Vitis, Allorhizobium vitis, Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, Genetic diversity, Phylogenetic tree, biology, 030306 microbiology, Genetic Variation, General Medicine, Agrobacterium tumefaciens, Rhizobium rhizogenes, biology.organism_classification, grapevine, Morocco, Phylogenetic diversity, Crown gall, phylogenetic diversity, Genome, Bacterial, Biotechnology
Abstract: Early Access: DEC 2019; International audience; AIMS: Crown gall, a phytobacteriosis characterized by the formation of tumours on plant roots was observed in recently planted vineyards of the Meknes region (Morocco). The objective of this research was to analyze the diversity of pathogenic agrobacteria isolated from grapevine in Morocco. METHODS AND RESULTS: Eighty-two isolates from 11 affected vineyards were characterized by recA sequencing and were found to belong to A. tumefaciens genomospecies G1, G4 or G7, Rhizobium rhizogenes, and to Allorhizobium vitis. Only the A. vitis isolates appeared to be pathogenic on tomato and MLSA phylogenetic analyses revealed a weak genetic diversity, with the definition of only four genomic groups. Definition of the A. vitis genomic groups correlateds with specific pathogenic traits: indeed, genomic groups differed with respect to the severity of hypersensitive response symptoms on tobacco leaves, the intensity of necrotic response on grapevine explants, and opine profiles. Both vitopine and octopine were detected by UHPLC in tumors induced by isolates of three genomic groups, an opine signature scarcely ever reported. CONCLUSIONS: Allorhizobium vitis is the only causative agent of crown gall on grape in Morocco, pathogenic isolates can be separated into four genomic groups. SIGNIFICANCE AND IMPACT OF THE STUDY: This study of recently crown-gall-infested vineyards demonstrated that Allorhizobium vitis is the only causative agent and revealed the presence of non-pathogenic Agrobacterium strain within tumors. Moreover, as the genetic diversity of the A. vitis isolates is relatively narrow, this study lays the basis for further analyses on the evolution of the disease, on the dissemination of the pTi and more globally on the fate of the different genomic groups in this newly colonized environment.
Published: 2020

14. Impact of

Author: Lidiane, Miotto-Vilanova, Barbara, Courteaux, Rosa, Padilla, Fanja, Rabenoelina, Cédric, Jacquard, Christophe, Clément, Gilles, Comte, Céline, Lavire, Essaïd, Ait Barka, Isabelle, Kerzaon, and Lisa, Sanchez
Subjects: Antifungal Agents, phenolic compounds, Plant Roots, Mass Spectrometry, Article, Gene Expression Regulation, Plant, Vitis, Chromatography, High Pressure Liquid, Phenylalanine Ammonia-Lyase, Plant Proteins, Flavonoids, Principal Component Analysis, beneficial bacterium, Burkholderiaceae, fungi, food and beverages, Discriminant Analysis, Polyphenols, qRT-PCR, Spores, Fungal, Plant Leaves, Vitis vinifera, Metabolome, Botrytis, UHPLC-UV/DAD-MS QTOF, Acyltransferases
Abstract: Phenolic compounds are implied in plant-microorganisms interaction and may be induced in response to plant growth-promoting rhizobacteria (PGPRs). Among PGPR, the beneficial bacterium Paraburkholderia phytofirmans PsJN was previously described to stimulate the growth of plants and to induce a better adaptation to both abiotic and biotic stresses. This study aimed to investigate the impact of PsJN on grapevine secondary metabolism. For this purpose, gene expression (qRT-PCR) and profiling of plant secondary metabolites (UHPLC-UV/DAD-MS QTOF) from both grapevine root and leaves were compared between non-bacterized and PsJN-bacterized grapevine plantlets. Our results showed that PsJN induced locally (roots) and systemically (leaves) an overexpression of PAL and STS and specifically in leaves the overexpression of all the genes implied in phenylpropanoid and flavonoid pathways. Moreover, the metabolomic approach revealed that relative amounts of 32 and 17 compounds in roots and leaves, respectively, were significantly modified by PsJN. Once identified to be accumulated in response to PsJN by the metabolomic approach, antifungal properties of purified molecules were validated in vitro for their antifungal effect on Botrytis cinerea spore germination. Taking together, our findings on the impact of PsJN on phenolic metabolism allowed us to identify a supplementary biocontrol mechanism developed by this PGPR to induce plant resistance against pathogens.
Published: 2019

15. Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogen Agrobacterium tumefaciens

Author: Céline Lavire, Loïc Marty, Yves Dessaux, Thibault Meyer, Armelle Vigouroux, Magali Aumont-Nicaise, Solange Moréra, Franck Pelissier, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche Centre National de la Recherche Scientifique (CNRS)French National Research Agency (ANR) ANR-12-BSV8-0003-01/02/03FRISBI ANR-10-INSB-05-01I2BC mass spectrometry SICaPS platform, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Bio-inspired Chemistry and Ecological Innovations (ChimEco), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: [SDV]Life Sciences [q-bio], opine, Opine, ATP-binding cassette transporter, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Ti plasmid, crystal structures, octopine, periplasmic binding protein, crown-gall, gene, Molecular Biology, Gene, transformed plants, 030304 developmental biology, degradation, Octopine, 0303 health sciences, region, biology, Catabolism, 030302 biochemistry & molecular biology, catabolism, Cell Biology, Agrobacterium tumefaciens, biology.organism_classification, agrobacterium tumefaciens, cyclase, ti-plasmid, chemistry, mannopinic acid, affinity, Bacteria
Abstract: Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. The mannityl-opine family encompasses mannopine, mannopinic acid, agropine and agropinic acid. These opines serve as nutrients and are imported into bacteria via periplasmic-binding proteins (PBPs) in association with ABC transporters. Structural and affinity data on agropine and agropinic acid opines bound to PBPs are currently lacking. Here, we investigated the molecular basis of AgtB and AgaA, proposed as the specific PBP for agropine and agropinic acid import, respectively. Using genetic approaches and affinity measurements, we identified AgtB and its transporter as responsible for agropine uptake in agropine-assimilating agrobacteria. Nonetheless, we showed that AgtB binds agropinic acid with a higher affinity than agropine, and we structurally characterized the agropinic acid-binding mode through three crystal structures at 1.4, 1.74 and 1.9 Å resolution. In the crystallization time course, obtaining a crystal structure of AgtB with agropine was unsuccessful due to the spontaneous lactamization of agropine into agropinic acid. AgaA binds agropinic acid only with a similar affinity in nanomolar range as AgtB. The structure of AgaA bound to agropinic acid at 1.65 Å resolution defines a different agropinic acid-binding signature. Our work highlights the structural and functional characteristics of two efficient agropinic acid assimilation pathways, of which one is also involved in agropine assimilation.
Published: 2019

16. Ecological conditions and molecular determinants involved in agrobacterium lifestyle in tumors

Author: Céline Lavire, Clémence Thiour-Mauprivez, Ludovic Vial, Thibault Meyer, Gilles Comte, Florence Wisniewski-Dyé, Isabelle Kerzaon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), CNRS (Mission pour l'interdisciplinarite, Agromics 2014-2016), French national program EC2CO-Biohefect/Ecodyn/Dril/MicrobiEn (IBAD), and French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche
Subjects: crown gall, galle du collet, Agrobacterium, [SDV]Life Sciences [q-bio], Virulence, Plant Science, Disease, lcsh:Plant culture, 03 medical and health sciences, plant defense, Plant defense against herbivory, Agrobacterium tumefaciens, tumor lifestyle, molecular traits, competition, Gall, lcsh:SB1-1110, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Rhizosphere, biology, 030306 microbiology, fungi, food and beverages, biology.organism_classification, agrobacterium tumefaciens, bacteria, compétition, Bacteria
Abstract: International audience; The study of pathogenic agents in their natural niches allows for a better understanding of disease persistence and dissemination. Bacteria belonging to the Agrobacterium genus are soil-borne and can colonize the rhizosphere. These bacteria are also well known as phytopathogens as they can cause tumors (crown gall disease) by transferring a DNA region (T-DNA) into a wide range of plants. Most reviews on Agrobacterium are focused on virulence determinants, T-DNA integration, bacterial and plant factors influencing the efficiency of genetic transformation. Recent research papers have focused on the plant tumor environment on the one hand, and genetic traits potentially involved in bacterium-plant interactions on the other hand. The present review gathers current knowledge about the special conditions encountered in the tumor environment along with the Agrobacterium genetic determinants putatively involved in bacterial persistence inside a tumor. By integrating recent metabolomic and transcriptomic studies, we describe how tumors develop and how Agrobacterium can maintain itself in this nutrient-rich but stressful and competitive environment.
Published: 2019

17. Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogen

Author: Loïc, Marty, Armelle, Vigouroux, Magali, Aumont-Nicaise, Franck, Pelissier, Thibault, Meyer, Céline, Lavire, Yves, Dessaux, and Solange, Moréra
Subjects: Structure-Activity Relationship, Bacterial Proteins, Protein Domains, Agrobacterium tumefaciens, Oxazines, ATP-Binding Cassette Transporters, Biological Transport, Mannitol
Published: 2018

18. The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum

Author: Céline Lavire, Magali Aumont-Nicaise, Gilles Comte, Solange Moréra, Thibault Meyer, Ludovic Vial, Armelle Vigouroux, Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Département Biochimie, Biophysique et Biologie Structurale (B3S), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Microbiologie et enzymologie structurale (MESB3S), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Mesures d'interactions protéine-protéine (PIM), Département Plateforme (PF I2BC), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), FRISBI ANR-10-INSB-05-01, and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Protein Conformation, [SDV]Life Sciences [q-bio], ATP-binding cassette transporter, crystal structure, sugar transport, bacteria, ABC transporter, microbiology, agrobacterium, galactinol, periplasmic binding protein, RFOs, plant defense, Agrobacterium fabrum, Crystallography, X-Ray, Disaccharides, Biochemistry, chemistry.chemical_compound, Plant defense against herbivory, Raffinose, MESB3S, bactérie, Rhizosphere, food and beverages, Plants, Protein Structure and Folding, PF, rhizosphère, B3S, agent pathogène, Agrobacterium, 030106 microbiology, Biology, Stachyose, 03 medical and health sciences, Bacterial Proteins, oligosaccharide, Melibiose, Molecular Biology, fungi, Nutrients, Cell Biology, biology.organism_classification, PIM, chemistry, Agrobacterium tumefaciens, Galactose
Abstract: The bacterial plant pathogen Agrobacterium fabrum uses periplasmic-binding proteins (PBPs) along with ABC transporters to import a wide variety of plant molecules as nutrients. Nonetheless, how A. fabrum acquires plant metabolites is incompletely understood. Using genetic approaches and affinity measurements, we identified here the PBP MelB and its transporter as being responsible for the uptake of the raffinose family of oligosaccharides (RFO), which are the most widespread d-galactose–containing oligosaccharides in higher plants. We also found that the RFO precursor galactinol, recently described as a plant defense molecule, is imported into Agrobacterium via MelB with nanomolar range affinity. Structural analyses and binding mode comparisons of the X-ray structures of MelB in complex with raffinose, stachyose, galactinol, galactose, and melibiose (a raffinose degradation product) revealed how MelB recognizes the nonreducing end galactose common to all these ligands and that MelB has a strong preference for a two-unit sugar ligand. Of note, MelB conferred a competitive advantage to A. fabrum in colonizing the rhizosphere of tomato plants. Our integrative work highlights the structural and functional characteristics of melibiose and galactinol assimilation by A. fabrum, leading to a competitive advantage for these bacteria in the rhizosphere. We propose that the PBP MelB, which is highly conserved among both symbionts and pathogens from Rhizobiace family, is a major trait in these bacteria required for early steps of plant colonization.
Published: 2018

19. Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

Author: Céline Lavire, David Chapulliot, Abdelkarim Filali-Maltouf, H. S. Gehlot, Antoine Le Quéré, José-Antonio Munive, Sonam Rathi, Guadalupe Rocha, Marine Rohmer, Nisha Tak, Ilham Sakrouhi, Thibault Meyer, Dany Severac, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V de Rabat [Agdal], BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Instituto de Ciencias, Benemérita Universidad Autónoma, Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Project SEP-CONACYT-ANUIES-ECOS NORD France [M08-A02], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Le Quéré, Antoine, Université Mohammed V de Rabat [Agdal] (UM5), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes ( LSTM ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université Montpellier 1 ( UM1 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Université Mohammed 5 Agdal, Université de Lyon (COMUE), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Montpellier GenomiX, and Institut de Génomique Fonctionnelle
Subjects: 0301 basic medicine, Biodiversité et Ecologie, bactérie fixatrice d'azote, sinorhizobium, adaptation, comparative genomics, Genome, mexique, rhizobium, maroc, octopine, Desert, Rhizobium-legume symbiosis, Phylogeny, High-Throughput Nucleotide Sequencing, asie, afrique, Genomics, legume, rhizobium-legume symbiosis, analyse phylogeographique, Phenotype, Sinorhizobium, ensifer, desert, Nitrogen fixation, Rhizobium, Desert Climate, Genome, Plant, Research Article, Biotechnology, nopaline, Asia, 030106 microbiology, interaction hôte symbiote, Biology, Synteny, légumineuse, amérique, Evolution, Molecular, Biodiversity and Ecology, 03 medical and health sciences, analyse de génome, Symbiosis, Phylogenetics, Nitrogen Fixation, Botany, Genetics, Adaptation, basicity, Comparative genomics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Desert climate, désert, Computational Biology, Molecular Sequence Annotation, 15. Life on land, biology.organism_classification, inde, Ensifer, 030104 developmental biology, inositol, Africa, america, profilage génétique, alcalinité, Americas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Rhizobium- legume symbiosis
Abstract: Background Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. Results Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer. Comparison of its core genome with those of E. meliloti, E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis. Conclusions The genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi. The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses. Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3447-y) contains supplementary material, which is available to authorized users.
Published: 2017

20. Essential oils of Origanum compactum and Thymus vulgaris exert a protective effect against the phytopathogen Allorhizobium vitis

Author: Isabelle Kerzaon, Rachid Benkirane, Khaoula Habbadi, Vincent Gaillard, El Hassan Achbani, Céline Lavire, Ludovic Vial, Thibault Meyer, Abdellatif Benbouazza, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut national de la recherche agronomique [Maroc] (INRA Maroc), Université Ibn Tofail [Kenitra], Partenaires INRAE, project 'Biological control of Agrobacterium vitis, the causal agent of Crown gall on grapevines' PRAD 14-08, regional center of the National Institute for Agricultural Research Meknes (INRA), and French national programme EC2CO-Biohefect/Ecodyn//Dril/MicrobiEn (IBAD)
Subjects: 0106 biological sciences, 0301 basic medicine, Agrobacterium, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], 030106 microbiology, Thymus vulgaris, Biological pest control, Microbial Sensitivity Tests, 01 natural sciences, Thymus Plant, Origanum compactum, 03 medical and health sciences, chemistry.chemical_compound, Rhizobiaceae, Origanum, Oils, Volatile, Plant Oils, Environmental Chemistry, Gall, Vitis, Carvacrol, Allorhizobium vitis, Thymol, Plant Diseases, 2. Zero hunger, biology, Traditional medicine, Inoculation, food and beverages, Biocontrol, General Medicine, biology.organism_classification, Pollution, Anti-Bacterial Agents, Crown gall, chemistry, Essential oils, Monoterpenes, Cymenes, Bacteria, 010606 plant biology & botany
Abstract: International audience; Allorhizobium (Agrobacterium) vitis is a host-specific pathogenic bacterium that causes grapevine crown gall disease, affecting vine growth and production worldwide. The antibacterial activities of different aromatic plant essential oils were tested in vitro and in planta against A. vitis. Among the essential oils tested, those of Origanum compactum and Thymus vulgaris showed the most significant in vitro antibacterial activities, with a MIC of 0.156 and 0.312 mg/mL, respectively. A synergistic effect of these two essential oils (1:1) was observed and confirmed by the checkerboard test. Carvacrol (61.8%) and thymol (47.8%) are, respectively, the major compounds in the essential oils of O. compactum and T. vulgaris and they have been shown to be largely responsible for the antibacterial activities of their corresponding essential oils. Results obtained in vitro were reinforced by an in planta pathogenicity test. A mixture of O. compactum and T. vulgaris essential oils (1:1), inoculated into the injured stem of a tomato plant and a grapevine at 0.312 mg/mL as a preventive treatment, reduced both the number of plants developing gall symptoms and the size of the tumors.
Published: 2017

21. Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum

Author: Florence Hommais, Ludovic Vial, Camille Villard, Jessica Baude, Xavier Nesme, Céline Lavire, Tony Campillo, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), EcoGenome project of the French Agence Nationale de la Recherche ANR-BLAN 08-0090, French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)
Subjects: 0301 basic medicine, Siderophore, Coumaric Acids, Operon, Iron, Siderophores, Genetics and Molecular Biology, Applied Microbiology and Biotechnology, Ferulic acid, 03 medical and health sciences, chemistry.chemical_compound, Gene expression, Gene, Biotransformation, Regulation of gene expression, chemistry.chemical_classification, Ecology, biology, Chemistry, Gene Expression Profiling, Bacterial, Agrobacterium tumefaciens, Gene Expression Regulation, Bacterial, Hydroxycinnamic acid, biology.organism_classification, Microarray Analysis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Culture Media, 030104 developmental biology, Biochemistry, Gene Expression Regulation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Metabolic Networks and Pathways, Food Science, Biotechnology
Abstract: The rhizosphere-inhabiting species Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (HCAs), especially ferulic acid and p -coumaric acid, via the novel A. fabrum HCA degradation pathway. Gene expression profiles of A. fabrum strain C58 were investigated in the presence of HCAs, using a C58 whole-genome oligoarray. Both ferulic acid and p -coumaric acid caused variations in the expression of more than 10% of the C58 genes. Genes of the A. fabrum HCA degradation pathway, together with the genes involved in iron acquisition, were among the most highly induced in the presence of HCAs. Two operons coding for the biosynthesis of a particular siderophore, as well as genes of the A. fabrum HCA degradation pathway, have been described as being specific to the species. We demonstrate here their coordinated expression, emphasizing the interdependence between the iron concentration in the growth medium and the rate at which ferulic acid is degraded by cells. The coordinated expression of these functions may be advantageous in HCA-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. The present results confirm that there is cooperation between the A. fabrum -specific genes, defining a particular ecological niche. IMPORTANCE We previously identified seven genomic regions in Agrobacterium fabrum that were specifically present in all of the members of this species only. Here we demonstrated that two of these regions, encoding the hydroxycinnamic acid degradation pathway and the iron acquisition pathway, were regulated in a coordinated manner. The coexpression of these functions may be advantageous in hydroxycinnamic acid-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. These data support the view that bacterial genomic species emerged from a bacterial population by acquiring specific functions that allowed them to outcompete their closest relatives. In conclusion, bacterial species could be defined not only as genomic species but also as ecological species.
Published: 2016

22. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Author: Ying Wang, Chantal Schenowitz, Jeffrey P. Tomkins, Claudine Médigue, Luis Gabriel Wall, Claudio Valverde, Benoit Cournoyer, Nadia Demange, Philippe Normand, Alison M. Berry, Louis S. Tisa, Juliana E. Mastronunzio, David Vallenet, David R. Benson, Pascal Lapierre, Emilie Bagnarol, Tania Rawnsley, Nathalie Choisne, Zoé Rouy, Johann Peter Gogarten, Céline Lavire, Alla Lapidus, Nicole Alloisio, Vincent Daubin, Arnaud Couloux, Stéphane Cruveiller, Ying Huang, Carla A. Bassi, James Niemann, Maria Pilar Francino, Derek M. Bickhart, J Maréchal, Laurent Labarre, Beth C. Mullin, Fernando Tavares, Olga R. Kopp, Michele Martinez, Eugene Goltsman, Anita Sellstedt, Pierre Pujic, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Department of Molecular and Cell Biology, University of Connecticut (UCONN), Department of Microbiology, University of New Hampshire (UNH), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Department of Biochemistry & Cellular & Molecular Biology and the Genome Science & Technology Program, The University of Tennessee [Knoxville], Department of Biochemistry & Cellular 1 Molecular Biology and The Genome Science & Technology Program, Department of Plant Physiology, Umeå University, Genomics Institute, Clemson University, Departamento de Ciencia y Tecnología [Buenos Aires], Universidad Nacional de Quilmes (UNQ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), University of Connecticut ( UCONN ), University of New Hampshire ( UNH ), University of California [Davis] ( UC Davis ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Programa Interacciones Biologicas, Departamento de Cienca y Tecnologia, Universidad Nacional de Quilmes, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), and University of California (UC)-University of California (UC)
Subjects: DNA, Bacterial, Root nodule, Prophages, [SDE.BE.ECOM]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Molecular Sequence Data, Frankia, Plant Roots, Genome, Article, Actinobacteria, Evolution, Molecular, Magnoliopsida, 03 medical and health sciences, Symbiosis, Gene Duplication, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, Phylogeny, Genetics (clinical), 030304 developmental biology, 2. Zero hunger, Frankia alni, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Facultative, Geography, biology, 030306 microbiology, fungi, food and beverages, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], DNA Transposable Elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Actinorhizal plant, [ SDE.BE.ECOM ] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Gene Deletion, Genome, Bacterial
Abstract: Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
Published: 2006

23. Selection of Unusual Actinomycetal Primary σ 70 Factors by Plant-Colonizing Frankia Strains

Author: Didier Blaha, Benoit Cournoyer, Céline Lavire, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: [SDV]Life Sciences [q-bio], Lineage (evolution), Molecular Sequence Data, Frankia, Sigma Factor, Biology, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, Plant Microbiology, Phylogenetics, Genomic library, Selection, Genetic, Gene, Phylogeny, Plant Diseases, 030304 developmental biology, Genetics, 0303 health sciences, Elaeagnaceae, Base Sequence, Ecology, Phylogenetic tree, 030306 microbiology, DNA-Directed RNA Polymerases, Gene Expression Regulation, Bacterial, Sequence Analysis, DNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, chemistry, Molecular phylogenetics, DNA, Food Science, Biotechnology
Abstract: Functional adaptations of σ 70 transcriptional factors led to the emergence of several paralogous lineages, each one being specialized for gene transcription under particular growth conditions. Screening of a Frankia strain EaI-12 gene library by σ 70 DNA probing allowed the detection and characterization of a novel actinomycetal primary (housekeeping) σ 70 factor. Phylogenetic analysis positioned this factor in the RpoD cluster of proteobacterial and low-G+C-content gram-positive factors, a cluster previously free of any actinobacterial sequences. σ 70 DNA probing of Frankia total DNA blots and PCR screening detected one or two rpoD -like DNA regions per species. rpoD matched the conserved region in all of the species tested. The other region was found to contain sigA , an alternative primary factor. sigA appeared to be strictly distributed among Frankia species infecting plants by the root hair infection process. Both genes were transcribed by Frankia strain ACN14a grown in liquid cultures. The molecular phylogeny of the σ 70 family determined with Frankia sequences showed that the alternative actinomycetal factors and the essential ones belonged to the same radiation. At least seven distinct paralogous lineages were observed among this radiation, and gene transfers were detected in the HrdB actinomycetal lineage.
Published: 2004

24. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov

Author: Kristina Lindström, Xavier Nesme, Seyed Abdollah Mousavi, Philippe de Lajudie, Céline Lavire, Lars Paulin, Janina Österman, Ludovic Vial, Niklas Wahlberg, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Food and Environmental Sciences, Academy of Finland [132544], Alfred Kordelin Foundation, Center for International Mobility (CIMO), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: MLSA, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, food.ingredient, Rhizobiaceae, Agrobacterium, [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Applied Microbiology and Biotechnology, Microbiology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Rhizobium galegae, food, Genus, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Clade, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Phylogeny, Ecology, Evolution, Behavior and Systematics, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Housekeeping genes, Phylogenetic tree, biology, ta1183, Rhizobium rhizogenes, biology.organism_classification, Allorhizobium, Genes, Bacterial, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Neorhizobium, ta1181, bacteria, Multilocus Sequence Typing
Abstract: Supplementary data; International audience; The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the "R. galegae complex" (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.
Published: 2014

25. Analysis of hydroxycinnamic acid degradation in Agrobacterium fabrum reveals a coenzyme A-dependent, beta-oxidative deacetylation pathway

Author: Sébastien Renoud, Cécile Chamignon, Florence Hommais, Jessica Baude, Isabelle Kerzaon, Céline Lavire, Ludovic Vial, Tony Campillo, Xavier Nesme, Floriant Bellvert, Vincent Gaillard, Gilles Comte, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Synthèse et étude de systèmes à intêret biologique (SEESIB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Matériaux Polymères (IMP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Ingénierie des Matériaux Polymères - Site INSA Lyon ( IMP ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Lyon, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, EcoGenome project of the French Agence Nationale de la Recherche [ANR-BLAN-08-0090], French Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Coumaric Acids, Agrobacterium, Coenzyme A, [SDV]Life Sciences [q-bio], [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, Genetics and Molecular Biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Applied Microbiology and Biotechnology, Protocatechuic acid, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Ferulic acid, 03 medical and health sciences, chemistry.chemical_compound, Vanillic acid, Caffeic acid, Hydroxybenzoates, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Biotransformation, 030304 developmental biology, chemistry.chemical_classification, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, biology, 030306 microbiology, Agrobacterium tumefaciens, 15. Life on land, Plants, biology.organism_classification, Hydroxycinnamic acid, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, chemistry, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Metabolic Networks and Pathways, Food Science, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The soil- and rhizosphere-inhabiting bacterium Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genes atu1416 , atu1417 , and atu1420 have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes atu1415 and atu1421 have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that the A. fabrum hydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transform p -coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.
Published: 2014

26. Rapid and Efficient Methods to Isolate, Type Strains and Determine Species of Agrobacterium spp. in Pure Culture and Complex Environments

Author: Malek Shams, Xavier Nesme, Tony Campillo, Daniel Muller, Ludovic Vial, Céline Lavire, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Jose J. Jimenez-Lopez (Editeur), ProdInra, Migration, and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: 2. Zero hunger, 0303 health sciences, Rhizosphere, STRUCTURE DU GENOME, biology, 030306 microbiology, Agrobacterium, [SDV]Life Sciences [q-bio], fungi, Alphaproteobacteria, food and beverages, 15. Life on land, GENETIQUE, Rhizobacteria, biology.organism_classification, [SDV] Life Sciences [q-bio], 03 medical and health sciences, Ti plasmid, Plasmid, Botany, Gall, TAXANOMIE, Bacteria, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, and as a general trait of the whole taxon, they are rhizospheric bacteria saprophytically living in the root environment (i.e. rhizosphere) of numerous plants. Rhizospheric interactions are generally considered to be of commensal type with no detrimental effect to the plant, but in most instances they are likely beneficial to plants. For evident agronomic purposes it is worthwhile to explore whether agrobacteria are themselves plant growth-promoting rhizobacteria (PGPR) or not. However, this requires an expert determination of the Agrobacterium taxonomy. Indeed our current investigations suggest that only some agrobacterial species from the abundant soil Agrobacterium guild are selected in the rhizosphere of a given plant. Secondly, but only when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots (Pitzscke & Hirt, 2010). Ti plasmids are conjugative and can easily spread in indigenous soil agrobacteria. As a result transconjugant agrobacteria become in turn pathogenic, contributing both to disease spread and perennial soil contamination. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. A set of biochemical and molecular methods were thus set up to facilitate the taxonomic assessment of agrobacteria either in pure culture or directly from complex environments such as soils, rhizospheres or tumours. After a presentation of the present state of Agrobacterium taxonomy, this work provides efficient methods to : i) isolate agrobacteria from complex environments thanks to elective media; ii) determine the Agrobacterium genus status of newly isolated strains on the basis of a minimal set of biochemical tests; iii) determine species and type novel isolates of Agrobacterium by sequence analysis of relevant marker genes; iv) determine amplicon content and genome architecture; v) detect the presence of Agrobacterium and Ti or Ri plasmid directly in complex environments by PCR using selected primers and metagenomic DNA extracted from whole bacterial communities.
Published: 2012

27. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Author: Daniel Muller, Malek Shams, Céline Lavire, Christine Oger-Desfeux, Xavier Nesme, Jessica Baude, Laurent Guéguen, Ludovic Vial, Denis Costechareyre, Tony Campillo, Danis Abrouk, Vincent Daubin, Florent Lassalle, Florence Hommais, David Chapulliot, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Microbiologie, adaptation et pathogénie (MAP), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Pôle Rhône-Alpin de BioInformatique [Lyon] (PRABI), Université de Lyon-Université de Lyon, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), PRABI, and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: AD-HOC-COMMITTEE, EVOLUTIONARY BIOLOGY, Adaptation, Biological, Agrobacterium, Genome, C58, bacterial species, GENETICS & HEREDITY, Research Articles, Phylogeny, Genetics, bactérie, évolution biologique, 0303 health sciences, biology, TI PLASMIDS, Ecology, Genomovar, Genomics, FAMILY, BACTERIA, Life Sciences & Biomedicine, Species complex, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], GENES, Genetic Speciation, Molecular Sequence Data, linear chromosome, bacterial evolution, Evolution, Molecular, 03 medical and health sciences, 0603 Evolutionary Biology, Bacterial Proteins, phylogénie, ecological niche, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Ecological niche, 0604 Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, écologie microbienne, Science & Technology, 030306 microbiology, biology.organism_classification, EVOLUTION, SP NOV, RHIZOBIUM-LEGUMINOSARUM, Agrobacterium tumefaciens, Hypothetical species, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, FERULIC ACID, Genome, Bacterial, Developmental Biology
Abstract: International audience; The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome--one on the circular chromosome and six on the linear chromosome--suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.
Published: 2011

28. Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity

Author: Céline Lavire, Franck Bertolla, David Chapulliot, Perrine Portier, Ali Rhouma, Denis Costechareyre, Xavier Nesme, Yves Dessaux, and Ali Boubaker
Subjects: Agrobacterium vitis, Rhizobiaceae, Agrobacterium, Sequence analysis, Biovar, Molecular Sequence Data, Soil Science, Microbiology, 03 medical and health sciences, Bacterial Proteins, Amplified Fragment Length Polymorphism Analysis, Ecology, Evolution, Behavior and Systematics, Alleles, Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, Ecology, biology, 030306 microbiology, food and beverages, Genetic Variation, Agrobacterium tumefaciens, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Rhizobium rhizogenes, Bacterial Typing Techniques, Rec A Recombinases, bacteria, Amplified fragment length polymorphism, Rhizobium
Abstract: The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one “former” Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.
Published: 2010

29. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Author: David Bruce, William S. Adney, Ravi D. Barabote, Gary Xie, Rebecca E. Parales, Philippe Normand, Thomas Brettin, Anamaria Necsulea, David H. Leu, Alison M. Berry, Céline Lavire, Vincent Daubin, Jean F. Challacombe, Petar Pujic, Xin Clare Xu, Chris Detter, Claudine Médigue, Alla Lapidus, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), National Renewable Energy Laboratory, Golden, Department of Microbiology, Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Department of Plant Sciences [Davis, CA], University of California [Davis] ( UC Davis ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), University of California-University of California, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: DNA, Bacterial, Letter, Hot Temperature, Pseudogene, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Actinomycetales, Genetics, Gene, Genetics (clinical), 030304 developmental biology, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, 2. Zero hunger, Base Composition, Principal Component Analysis, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Ecology, 030306 microbiology, Thermophile, Prokaryote, Sequence Analysis, DNA, Chromosomes, Bacterial, 15. Life on land, Ribosomal RNA, biology.organism_classification, Adaptation, Physiological, Flagella, Proteome, Mobile genetic elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial
Abstract: We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three laterally-acquired genomic islands of likely ecophysiological value.
Published: 2009

30. Phase Variation and Genomic Architecture Changes in Azospirillum

Author: René Bally, Patrick Mavingui, Yvan Moënne-Loccoz, Jacqueline Haurat, Florence Wisniewski-Dyé, Céline Lavire, Ludovic Vial, Didier Blaha, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), and Delorme, Christine
Subjects: DNA, Bacterial, phenotypic switch, Molecular Sequence Data, PFGE, plasmid pattern, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, genome plasticity, Plant Roots, 03 medical and health sciences, Plant Microbiology, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Genetic variation, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, Soil Microbiology, 030304 developmental biology, 2. Zero hunger, Genetics, Phase variation, Gene Rearrangement, 0303 health sciences, Rhizosphere, Ralstonia solanacearum, biology, Base Sequence, 030306 microbiology, Genetic Variation, Oryza, Gene rearrangement, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Electrophoresis, Gel, Pulsed-Field, Rec A Recombinases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Azospirillum lipoferum, Replicon, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Azospirillum, Soil microbiology, Bacteria, Genome, Bacterial, Plasmids
Abstract: Azospirillum is a plant growth-promoting rhizobacterium associated with roots of monocots, including important crops, such as wheat, corn, and rice. Both in greenhouse and in field trials, Azospirillum was shown to exert beneficial effects on plant growth and crop yields, under various soil and climatic conditions (15). The actual benefit from biological nitrogen fixation has been questioned, and plant growth promotion by Azospirillum seems to be due mainly to production of phytohormones (9, 15). The most abundant phytohormone produced is indole-3-acetic acid, allowing an increase in the number of lateral roots and root hairs; this results in a higher absorption of water and minerals from the soil (9). Bacterial populations, especially in soil or in the rhizosphere, have to endure fluctuating environmental conditions. Bacteria have evolved different strategies to adapt to these environments. Phase variation is one adaptive process by which bacteria undergo frequent, usually reversible phenotypic changes resulting from genetic or epigenetic alterations at specific genetic loci (29). This process is used by several bacterial species to generate intrapopulation diversity that increases bacterial fitness and is important in niche adaptation or to escape host defenses (reviewed in references 46 and 55). In contrast to spontaneous mutations, which occur at a frequency of approximately 10−8 to 10−6 mutations per growing cell per generation, phase variation occurs at frequencies higher than 10−5 switches per cell per generation (29). Various mechanisms control phase variation. These include DNA inversion or duplication, deletion, transposition, homologous recombination, slipped-strand mispairing, and differential methylation (reviewed in reference 55). Phase variation in pathogenic bacteria—for example, switching of type IV pili in Neisseria gonorrhoeae (27), differential expression of surface layer proteins in Campylobacter fetus (16), and loss of virulence in the phytopathogen Ralstonia solanacearum (43)—has been extensively studied. However, phase variation is not restricted to pathogenic bacteria. Indeed, it also occurs during rhizosphere colonization of various plants by several strains of beneficial plant-associated Pseudomonas (1, 48). For instance, the regulation of biocontrol traits (production of antifungal metabolites, chitinases, and biosurfactants) by phase variation was reported for Pseudomonas spp. strains (54). Azospirillum lipoferum 4B, a strain isolated from a rice rhizosphere, generates in vitro at high frequencies (10−4 to 10−3 per cell per generation) a stable phase variant named 4VI (3, 30). Variant colonies are readily distinguishable from wild-type colonies by the differential absorption of dyes incorporated into the growth medium. The 4VI variant exhibits pleiotropic modifications; it gained assimilation of certain sugars but lost the ability to assimilate other sugars (3), to reduce triphenyl tetrazolium chloride, to bind some dyes, to swim (4), and to reduce nitrous oxide (our unpublished results). A. lipoferum 4T, a nonswimming strain displaying all of the features of the 4VI variant, and strain A. lipoferum 4B have been isolated simultaneously from rice rhizosphere at the same frequency (8). A. lipoferum 4T retains the ability to efficiently colonize rice roots (2). Like 4VI, A. lipoferum 4T was found to be genetically very close to A. lipoferum 4B (3, 8, 28), suggesting that A. lipoferum 4T could in fact be a 4VI variant of strain 4B generated within the soil ecosystem. We recently showed that inactivating recA in strain 4B resulted in a higher frequency of generation of variants (57), contrasting with many studies of other bacteria showing either no effect or the abolition of phase variation process in recA mutants. This finding suggests the possibility that phase variation is accompanied by genetic rearrangements. As of now, the molecular mechanism underlying these nonreversible changes in A. lipoferum 4B remains to be determined. In this study, the objective was to determine whether genomic rearrangements take place during phase variation of strain 4B and related Azospirillum strains. The current work shows that genomic rearrangements are concomitant with phase variation in three species of Azospirillum.
Published: 2006

31. Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox

Author: Irina A. Alekhina, Jean-Robert Petit, Jean-Louis Birrien, Serguey Bulat, Céline Lavire, Philippe Normand, Daniel Prieur, Catherine Hänni, Pascale Fournier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Saint Petersburg Nuclear Physics Institute RAS, St Petersburg Nuclear Physics Institute, Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire de glaciologie et géophysique de l'environnement ( LGGE ), Observatoire des Sciences de l'Univers de Grenoble ( OSUG ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de microbiologie des environnements extrêmophiles ( LM2E ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Brest ( UBO ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Centre de génétique et de physiologie moléculaire et cellulaire ( CGPhiMC ), Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS )
Subjects: Geological Phenomena, Molecular Sequence Data, Geochemistry, Antarctic Regions, Microbiology, Polymerase Chain Reaction, 03 medical and health sciences, Ice core, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Ribosomal, 16S, Subglacial lake, Lake Vostok, Seawater, Hydrogenophilaceae, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, biology, Accretion (meteorology), 030306 microbiology, Ecology, Thermophile, RuBisCO, Ice, Sediment, Geology, 16S ribosomal RNA, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, biology.protein
Abstract: Summary The 3561 m Vostok ice core sample originating from the subglacial Lake Vostok accretion (frozen lake water) ice with sediment inclusions was thoroughly studied by various means to confirm the presence of the thermophile bacterium Hydrogenophilus thermoluteolus reported earlier in the 3607 m accretion ice sample. PCR and molecular-phylogenetic analyses performed in two independent laboratories were made using different 16S rRNA gene ( rrs ) targeted primers. As a result, rrs -targeted PCR permitted to recover several very closely related clones with a small genetic distance to Hydrogenophilus thermoluteolus ( < 1%). In addition, RubisCO ( cbbL or rbcL ) and NiFe-Hydrogenase (hoxV or hupL ) targeted PCR have also allowed to recover sequences highly related to Hydrogenophilus thermoluteolus . All these results point to the presence of thermophilic chemoautotrophic microorganisms in Lake Vostok accretion ice. They presumably originate from deep faults in the bedrock cavity containing the lake in which episodes of seismotectonic activity would release debris along with microbial cells.
Published: 2006

32. Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

Author: Benoit Cournoyer, Dominique Louis, Jérôme Briolay, Céline Lavire, Philippe Normand, Guy Perrière, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: DNA Replication, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Molecular Sequence Data, Frankia, Cloning vector, Replication Origin, Microbiology, Open Reading Frames, 03 medical and health sciences, Plasmid, Nitrogen Fixation, Actinomycetales, Genetics, Replicon, ORFS, Codon, Symbiosis, Molecular Biology, 030304 developmental biology, Frankia alni, 0303 health sciences, biology, 030306 microbiology, Sequence Analysis, DNA, biology.organism_classification, Open reading frame, Codon usage bias, Plasmids
Abstract: The actinomycete Frankia has never been transformed genetically. To favour the development of Frankia cloning vectors, we have fully sequenced the Frankia alni pFQ31 cryptic plasmid and performed analyses to characterise its coding and non-coding regions. This plasmid is 8551 bp-long and contains 72% G+C. Computer-assisted analyses identified 18 open reading frames (ORFs). These ORFs show a synonymous codon usage different from the one of Frankia chromosomal genes, suggesting an evolutionary bias linked to the nature of the replicon or a horizontal transfer. Three ORFs were found to encode genes likely to be involved in plasmid replication and stability: parFA (partition protein), ptrFA (transcriptional repressor of the GntR family) and repFA (initiation of replication). DNA signatures of a replication origin were identified in the ptrFA^repFA intergenic region. These structural motifs are similar to those observed among origins of iteron-containing plasmids replicating via a a mode. fl 2001 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Published: 2001

33. La dégradation des acides hydroxycinnamiques comme signal de perception de la plante : Régulation et rôle dans l’écologie d’Agrobacterium fabrum'

Author: Meyer, Thibault, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université Claude Bernard Lyon 1, Céline Lavire, Gilles Comte., Université de Lyon, and Gilles Comte
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, facteurs de transcription, régulation transcriptionnelle, agrobacterium, hydroxycinnamics acids (HCAs), agrobacterium fabrum, plant-bacteria interaction, interaction plantes-bactéries, acides hydroxycinnamiques, ecological transition, Transcriptionnal regulation, oligosaccharides de la famille du raffinose (RFO), oligosaccharides, raffinose family oligosaccharides (RFOs), transition écologique, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Thèse confidentielle jusqu'au 29 juin 2019.; Agrobacterium establish long term interactions with plants, either in a rhizosphere or pathogenic lifestyle. Pathogenic agrobacteria are causing the crown gall disease by genetically modifying the plant cells host, thus creating a specific ecological niche (tumor). The transition from the rhizosphere to the pathogenic lifestyle is triggered by bacterial perception of plant-derived signals, including hydroxycinnamic acids (HCAs) such as ferulic acid. However, A. fabrum strains have species-specific genes that allow HCAs degradation.We hypothesized that in A. fabrum, the degradation of the HCAs is perceived as a plant signal which influences important functions involved in the interaction with plants. We characterized the regulation of HCAs degradation, evaluated its role in the fitness of A. fabrum, and suggested its importance for the transition between the rhizosphere and pathogenic lifestyles. Then, we showed that the degradation of HCAs modulates carbon metabolism, such as the use of amino acids and sugars belonging to the raffinose family oligosaccharides (RFO). We have demonstrated that besides these sugars, the MelB protein allows the import melibiose and galactinol. Their use is important for plant colonization, since seed germination. The analyzes of gene expression and bacterial metabolism in the presence of a plant signal compound, revealed new determinants important for A. fabrum ecology, including transcription factors. In addition, it confirmed the importance of cellular exchanges and bacterial competition for Agrobacterium fitness in planta; Les agrobactéries établissent des relations à long terme avec les plantes et ce, dans deux styles de vie différents, rhizosphérique et pathogène (galle du collet). Dans ce mode de vie, les bactéries modifient génétiquement leur hôte et se créent ainsi une niche écologique spécifique (tumeur). La transition entre les deux styles de vie est déclenchée par la perception de signaux végétaux, parmi lesquels des acides hydroxycinnamiques (HCAs) comme l’acide férulique. Or dans l’espèce Agrobacterium fabrum, des gènes spécifiques permettent la dégradation des HCAs. Nous avons émis l’hypothèse que cette dégradation était un signal de proximité de la plante et influençait alors des fonctions importantes pour l’interaction avec celle-ci. Nous avons caractérisé la régulation de la dégradation des HCAs, évalué son rôle dans la valeur sélective d’A. fabrum, et suggéré son importance dans la transition entre les styles de vie rhizosphérique et pathogène. Nous avons montré que la dégradation des HCAs module le métabolisme carboné bactérien, notamment l’utilisation d’acide aminés et d’oligosaccharides de la famille du raffinose. Nous avons caractérisé la protéine MelB qui permet l’import de ces sucres, du mélibiose et du galactinol. Leur utilisation est importante pour la colonisation des plantes dès la germination. L’analyse de l’expression des gènes et du métabolisme bactérien en présence d'un composé signal de la plante, nous a révélé de nouveaux déterminants importants pour l’écologie de ce phytopathogène, notamment des facteurs de transcription. En outre, cette analyse a confirmé l’importance des échanges cellulaires et de déterminants impliqués dans la compétition bactérienne
Published: 2018

34. Degradation of hydroxycinnamic acids as signal of plant perception : regulation and role in the Agrobacterium fabrum ecology

Author: Meyer, Thibault, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université de Lyon, Céline Lavire, and Gilles Comte
Subjects: Agrobacterium fabrum, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecological transition, Oligosaccharides de la famille du raffinose (RFO), Transcriptionnal regulation, Régulation transcriptionnelle, Hydroxycinnamics acids (HCAs), Plant-bacteria interaction, Raffinose family oligosaccharides (RFOs), Transition écologique, Interaction plantes-bactéries, Acides hydroxycinnamiques
Abstract: Agrobacterium establish long term interactions with plants, either in a rhizosphere or pathogenic lifestyle. Pathogenic agrobacteria are causing the crown gall disease by genetically modifying the plant cells host, thus creating a specific ecological niche (tumor). The transition from the rhizosphere to the pathogenic lifestyle is triggered by bacterial perception of plant-derived signals, including hydroxycinnamic acids (HCAs) such as ferulic acid. However, A. fabrum strains have species-specific genes that allow HCAs degradation.We hypothesized that in A. fabrum, the degradation of the HCAs is perceived as a plant signal which influences important functions involved in the interaction with plants. We characterized the regulation of HCAs degradation, evaluated its role in the fitness of A. fabrum, and suggested its importance for the transition between the rhizosphere and pathogenic lifestyles. Then, we showed that the degradation of HCAs modulates carbon metabolism, such as the use of amino acids and sugars belonging to the raffinose family oligosaccharides (RFO). We have demonstrated that besides these sugars, the MelB protein allows the import melibiose and galactinol. Their use is important for plant colonization, since seed germination. The analyzes of gene expression and bacterial metabolism in the presence of a plant signal compound, revealed new determinants important for A. fabrum ecology, including transcription factors. In addition, it confirmed the importance of cellular exchanges and bacterial competition for Agrobacterium fitness in planta; Les agrobactéries établissent des relations à long terme avec les plantes et ce, dans deux styles de vie différents, rhizosphérique et pathogène (galle du collet). Dans ce mode de vie, les bactéries modifient génétiquement leur hôte et se créent ainsi une niche écologique spécifique (tumeur). La transition entre les deux styles de vie est déclenchée par la perception de signaux végétaux, parmi lesquels des acides hydroxycinnamiques (HCAs) comme l’acide férulique. Or dans l’espèce Agrobacterium fabrum, des gènes spécifiques permettent la dégradation des HCAs. Nous avons émis l’hypothèse que cette dégradation était un signal de proximité de la plante et influençait alors des fonctions importantes pour l’interaction avec celle-ci. Nous avons caractérisé la régulation de la dégradation des HCAs, évalué son rôle dans la valeur sélective d’A. fabrum, et suggéré son importance dans la transition entre les styles de vie rhizosphérique et pathogène. Nous avons montré que la dégradation des HCAs module le métabolisme carboné bactérien, notamment l’utilisation d’acide aminés et d’oligosaccharides de la famille du raffinose. Nous avons caractérisé la protéine MelB qui permet l’import de ces sucres, du mélibiose et du galactinol. Leur utilisation est importante pour la colonisation des plantes dès la germination. L’analyse de l’expression des gènes et du métabolisme bactérien en présence d'un composé signal de la plante, nous a révélé de nouveaux déterminants importants pour l’écologie de ce phytopathogène, notamment des facteurs de transcription. En outre, cette analyse a confirmé l’importance des échanges cellulaires et de déterminants impliqués dans la compétition bactérienne
Published: 2018

35. Assessing the diversity of agrobacterial populations

Author: Shams, Malek, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Université Claude Bernard - Lyon I, Xavier Nesme, Céline Lavire, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Pyroséquençage, Microdiversité bactérienne, food and beverages, Pyrosequencing, Agrobacterium, Détection par PCR, Identification des espèces, Agricultural sciences, Rhizobiaceae, Species identification, PCR detection, Bacterial community, Bacterial microdiversity, MALDI-TOF MS, Communauté bactérienne, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Sciences agricoles
Abstract: Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, they are rhizospheric bacteria saprophytically living in the rhizosphere of numerous plants and they are likely beneficial to plants. Secondly, when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. In this thesis we evaluated the usefulness of MALDI-TOF MS technique as a high throughput tool to determine and classify agrobacteria. Then we set up a recA-based PCR method to accurately and exhaustively assess agrobacterial diversity either of isolated agrobacteria or directly in various biotopes. We applied standard biochemical, recA-based and Ti plasmid-based identification methods to study the prevalence of pathogenic and non-pathogenic agrobacteria at the country and local scales. Finally, we tested whether analyzing the internal composition of recA amplicons could be a way to directly assess the micro-diversity of agrobacterial populations using cloning sequencing or pyrosequencing approaches. The later methodology was applied to establish the actual field diversity of Agrobacterium and to evaluate whether plant genotypes differentially select agrobacteria in their root systems, providing first data upon biotic factors shaping the population structure of agrobacteria, Les bactéries du genre Agrobacterium forment un ensemble taxonomiquement diversifié composé de nombreuses espèces, présent dans la plupart des sols et des rhizosphère. Les agrobactéries sont le plus souvent anodines voire stimulatrices de la croissance des plantes. Par contre, celles qui hébergent un plasmide Ti induisent la maladie de la galle du collet à de nombreuses plantes d'intérêt agronomique. Dans ce contexte, nous avons d'une part donné l'état actuel des connaissances sur la taxonomie du genre Agrobacterium, et nous avons fait une revue des méthodes d'isolement et de typage de ces bactéries. D'autre part, nous avons cherché à mettre au point des méthodes d'identification rapides et fiables des différentes espèces d'agrobactérie. La méthode de MALDI-TOF MS a permis d'identifier les espèces mais elle n'était pas assez résolutive pour typer des souches et encore moins la présence de plasmides Ti dans les isolats. Nous avons alors développé des amorces de PCR spécifiques de 17 espèces, du genre Agrobacterium et de la famille Rhizobiaceae. Ces amorces se sont révélées efficaces pour identifier les bactéries cultivées et aussi pour détecter leur présence dans des communautés microbiennes. Nous avons utilisé ces outils pour étudier la répartition des agrobactéries à l'échelle d'un pays, d'une station et entre sols nus et sols rhizosphériques en utilisant soit des isolats soit des ADN extraits des différents environnements. Enfin, nous avons montré que le clonage-séquençage ou le séquençage à haut débit d'amplicons obtenus à partir d'ADN de communautés microbiennes nous permettaient de connaître la diversité des populations d'agrobactéries
Published: 2012

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35 results on '"Céline Lavire"'

1. Biochemical and molecular identification of a native Bacillus thuringiensis gv. cytolyticus isolate with insecticidal effect against the pod borer larvae (Helicoverpa armigera)

2. Biological Control of Grapevine Crown Gall Disease, Caused by Allorhizobium vitis, Using Paraburkholderia phytofirmans PsJN

3. Paraburkholderia phytofirmans PsJN delays Botrytis cinerea development on grapevine inflorescences

4. Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

5. Ecological Conditions and Molecular Determinants Involved in Agrobacterium Lifestyle in Tumors

6. A simple and stable method of tagging Agrobacterium fabrum C58 for environmental monitoring

7. Impact of Paraburkholderia phytofirmans PsJN on Grapevine Phenolic Metabolism

8. Two Novel Species Isolated from Wheat Rhizospheres in Serbia: Pseudomonas Serbiensis Sp. Nov. And Pseudomonas Serboccidentalis Sp. Nov

9. Development and validation of a UHPLC-ESI-QTOF mass spectrometry method to analyze opines, plant biomarkers of crown gall or hairy root diseases

10. Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum

11. Development of a DNA-Based Real-Time PCR Assay To Quantify

12. Clarifying the taxonomy of the causal agent of bacterial leaf spot of lettuce through a polyphasic approach reveals that Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym of Xanthomonas hortorum Vauterin et al. 1995

13. Characterization and phylogenetic diversity of Allorhizobium vitis isolated from grapevine in Morocco

14. Impact of

15. Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogen Agrobacterium tumefaciens

16. Ecological conditions and molecular determinants involved in agrobacterium lifestyle in tumors

17. Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogen

18. The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum

19. Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

20. Essential oils of Origanum compactum and Thymus vulgaris exert a protective effect against the phytopathogen Allorhizobium vitis

21. Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum

22. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

23. Selection of Unusual Actinomycetal Primary σ 70 Factors by Plant-Colonizing Frankia Strains

24. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov

25. Analysis of hydroxycinnamic acid degradation in Agrobacterium fabrum reveals a coenzyme A-dependent, beta-oxidative deacetylation pathway

26. Rapid and Efficient Methods to Isolate, Type Strains and Determine Species of Agrobacterium spp. in Pure Culture and Complex Environments

27. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

28. Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity

29. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

30. Phase Variation and Genomic Architecture Changes in Azospirillum

31. Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox

32. Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

33. La dégradation des acides hydroxycinnamiques comme signal de perception de la plante : Régulation et rôle dans l’écologie d’Agrobacterium fabrum'

34. Degradation of hydroxycinnamic acids as signal of plant perception : regulation and role in the Agrobacterium fabrum ecology

35. Assessing the diversity of agrobacterial populations

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35 results on '"Céline Lavire"'

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