Author: "Xavier Nesme" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

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1. 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, Kasthuri Venkateswaran, California Institute of Technology (CALTECH), 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), Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark, Weill Cornell Medicine [New York], and The Wellcome Trust Sanger Institute [Cambridge]
Subjects: Microbiology (medical), MLSA, PHYLOGENY, CROWN-GALL, Microbiology, COLONIZATION, CLADE, 03 medical and health sciences, ALGORITHM, Agrobacterium tomkonis, 030304 developmental biology, Original Research, 0303 health sciences, metagenomics, IDENTIFICATION, 030306 microbiology, ISS, fungi, phylogenomics, biochemical phenomena, metabolism, and nutrition, TUMORS, QR1-502, DELINEATION, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, genomovar G3, bacteria, TUMEFACIENS, SPP
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

2. 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

3. Agrobacterium fabrum C58 involved nitrate reductase NapA and antisense RNA NorR to denitrify

Author: Solène Lecomte, Feth el Zahar Haichar, Mariane Pivard, Jeanne Doré, Camille Villard, Xavier Nesme, Florence Hommais, Ludovic Vial, Théophile Franzino, 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), Microbiologie, adaptation et pathogénie (MAP), 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 International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), La Federation de Recherche (FR) BioEnviS, Universite Lyon 1French Ministere de l'Education nationale de l'Enseignement Superieur et de la Recherche, ANR-18-CE32-0005,DIORE,Régulation de la dénitrification par la nature des exsudats racinaires(2018), La Federation de Recherche (FR) BioEnviS, Universite Lyon 1 French Ministere de l'Education nationale de l'Enseignement Superieur et de la Recherche, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-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), 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 International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Denitrification, nitrate reductase, Operon, [SDV]Life Sciences [q-bio], Denitrification pathway, Agrobacterium, Reductase, Biology, Nitrate reductase, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Nitrate, RNA, Antisense, small RNA, Nitrite, NapA, 2. Zero hunger, NAPA, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Nitrates, denitrification, Ecology, fitness, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, root colonization, 010606 plant biology & botany
Abstract: Agrobacterium fabrum C58 is a plant-associated bacterium that is able to denitrify under anoxic conditions. The cluster of denitrification genes harbored by this strain has been well characterized. It includes nir and nor operons encoding nitrite and nitric oxide reductases, respectively. However, the reductase involved in nitrate reduction has not yet been studied and little information is available on denitrification regulators in A. fabrum C58. In this study, we aimed to (i) characterize the nitrate reductase, (ii) determine its role in A. fabrum C58 fitness and root colonization and (ii) reveal the contribution of small RNA on denitrification regulation. By constructing a mutant strain defective for napA, we demonstrated that the reduction of nitrate to nitrite was catalyzed by the periplasmic nitrate reductase, NapA. We evidenced a positive role of NapA in A. fabrum C58 fitness and suggested that A. fabrum C58 is able to use components exuded by plant roots to respire anaerobically. Here, we showed that NorR small RNA increased the level of norCBQ mRNA and a decrease of NorR is correlated with a decrease in N2O emission. Together, our results underscore the importance of understanding the denitrification pathway at the strain level in order to develop strategies to mitigate N2O production at the microbial community level.
Published: 2020

4. 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

5. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Author: David Vallenet, Xavier Nesme, David Chapulliot, Alexandra Calteau, Laurent Guéguen, Daniel Muller, Valérie Barbe, Simon Penel, Ludovic Vial, Florent Lassalle, Vincent Daubin, Audrey Dubost, Rémi Planel, Thomas Bigot, Damien Mornico, 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), 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), 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), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Département de chimie organique, Université de Genève (UNIGE), French National Research Agency (ANR) [ANR-BLAN-08-0090, ANR-10-BINF-01-01], AGROMICS grant from the ENVIROMICS challenge of the Interdisciplinary Mission of the French National Centre for Scientific Research (CNRS), LABGeM (CEA/IG/Genoscope CNRS) [UMR8030], ANR [ANR-10-INBS-09], Lassalle, Florent, 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 Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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), Université de Genève = University of Geneva (UNIGE), 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 Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Genome evolution, Agrobacterium, 030106 microbiology, Biology, Genome, 03 medical and health sciences, 0603 Evolutionary Biology, Phylogenetics, Gene duplication, Genetics, Reverse ecology, Gene, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, 0303 health sciences, 0604 Genetics, Ecology, Phylogenetic tree, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ancestral genome, cotransferred genes, Computational Biology, Genetic Variation, High-Throughput Nucleotide Sequencing, HGT, tree reconciliation, 15. Life on land, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Evolution, reverse ecology, 030104 developmental biology, Agrobacterium tumefaciens, Horizontal gene transfer, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Adaptation, Genome, Bacterial, Software, Research Article, Developmental Biology
Abstract: Both the ecological adaptations of an organism and its evolutionary history are recorded in a genome. We used Agrobacterium biovar 1, a diverse group of plant-associated bacteria as a model to search for genomic signatures of ecological adaptation in relation to diversification. We designed a new phylogenetic approach accounting for horizontal transfer and duplication to reconstruct the evolutionary history of Agrobacterium genomes and infer ancestral gene contents. We find that allowing for genes to be co-transferred and co-duplicated significantly improves scenarios of genome evolution. Most genes acquired before the diversification of major clades within Agrobacterium are organized in blocks of co-evolving genes encoding coherent pathways. This pattern of gene co-evolution rejects a neutral model of transfer, in which neighbouring genes would be transferred independently of their function. In addition, the conservation of acquired genes is driven by purifying selection on collectively coded functions. Based on this criterion, we identify the genomic determinants of ecological niche diversification within this group. The strong selective role of host plant rhizospheres in the history of Agrobacterium is evident from the recurrent acquisition of functions involved in the production of secreted secondary metabolites or extracellular matrix, and in the metabolism of plant-derived compounds such as phenolics and amino-acids. Our reconstructed genome history - from single gene trees with transfer and duplication events to blocks of co-evolved genes and functional annotations, etc. - is compiled in an integrative database, Agrogenom, which can be visualized and queried through an interactive web interface accessible at http://phylariane.univ-lyon1.fr/db/agrogenom/3.
Published: 2017

6. Minimal standards for the description of new genera and species of rhizobia and agrobacteria

Author: Philippe de Lajudie, Nemanja Kuzmanović, Tomasz Stępkowski, Esperanza Martínez-Romero, Alvaro Peix, Peter Young, Xavier Nesme, Emma Theodora Steenkamp, Seyed Abdollah Mousavi, Gehong Wei, Julie Ardley, Lionel Moulin, Florent Lassalle, Pablo Vinuesa, Bertrand D. Eardly, Estelle Jumas-Bilak, Jerri Édson Zilli, Anne Willems, Kristina Lindström, Mitchell Andrews, Joanna Puławska, Chang Fu Tian, Ridha Mhamdi, 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), Peix, Álvaro, Peix, Álvaro [0000-0001-5084-1586], Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM), Hydrosciences Montpellier (HSM), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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: 0106 biological sciences, 0301 basic medicine, Systematics, Agrobacteria, [SDV]Life Sciences [q-bio], Agrobacterium, Guidelines as Topic, Rhizobia, Biology, rhizobia, 010603 evolutionary biology, 01 natural sciences, Microbiology, Genome, Minimal standards for taxonomy, 03 medical and health sciences, taxonomy, Terminology as Topic, Genetic variation, agrobacteria, Nomenclature, Ecology, Evolution, Behavior and Systematics, Whole genome sequencing, Human evolutionary genetics, Bacterial taxonomy, Genome-based taxonomy, General Medicine, 3. Good health, 030104 developmental biology, Evolutionary biology, genome-based, Taxonomy (biology), Rhizobium
Abstract: 12 páginas, Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee onSystematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updatedminimal standards for the description of new species (and genera) in these groups. The essential requirements (minimalstandards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidencefor differentiation from other species based on genome sequence comparisons. It is also recommended that (3) geneticvariation within the species is documented with sequence data from several clearly different strains and (4) phenotypicfeatures are described, and their variation documented with data from a relevant set of representative strains. Furthermore,it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevantgene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a namethat conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication eitherdirectly in theInternational Journal of Systematic and Evolutionary Microbiologyor in a validation list when publishedelsewhere, and (8) deposition of the type strain in two international culture collections in separate countries
Published: 2019

7. Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops

Author: Joanna Puławska, Nemanja Kuzmanović, Xavier Nesme, Kornelia Smalla, 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), 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: Crops, Agricultural, DNA, Bacterial, 0301 basic medicine, MLSA, Sub-clade "rubi\textquotedblright, Sequence analysis, Agrobacterium, [SDV]Life Sciences [q-bio], 030106 microbiology, Biology, DNA, Ribosomal, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Phylogenetics, Plant Tumors, RNA, Ribosomal, 16S, Botany, Gene, Phylogeny, Ecology, Evolution, Behavior and Systematics, Genes, Essential, Strain (biology), Fatty Acids, Nucleic Acid Hybridization, Whole-genome-based phylogeny, Sequence Analysis, DNA, 16S ribosomal RNA, rpoB, biology.organism_classification, Bacterial Typing Techniques, Housekeeping gene, Crown gall, 030104 developmental biology, Genes, Bacterial, ANI, bacteria, DDH, Multilocus Sequence Typing
Abstract: International audience; The plant tumorigenic strain NCPPB 1650T isolated from Rosa\texttimeshybrida, and four nonpathogenic strains isolated from tumors on grapevine (strain 384), raspberry (strain 839) and blueberry (strains B20.3 and B25.3) were characterized by using polyphasic taxonomic methods. Based on 16S rRNA gene phylogeny, strains were clustered within the genus Agrobacterium. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, recA and rpoB housekeeping genes indicated that five strains studied form a novel Agrobacterium species. Their closest relatives were Agrobacterium sp. R89-1, Agrobacterium rubi and Agrobacterium skierniewicense. Authenticity of the novel species was confirmed by average nucleotide identity (ANI) and in silico DNADNA hybridization (DDH) comparisons between strains NCPPB 1650T and B20.3, and their closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. Whole-genome-based phylogeny further supported distinctiveness of the novel species, that forms together with A. rubi, A. skierniewicense and Agrobacterium sp. R89-1 a well-delineated sub-clade of Agrobacterium spp. named "rubi\textquotedblright. As for other species of the genus Agrobacterium, the major fatty acid of the strains studied was 18:1 w7c (73.4278.12%). The five strains studied were phenotypically distinguishable from other species of the genus Agrobacterium. Overall, polyphasic characterization showed that the five strains studied represent a novel species of the genus Agrobacterium, for which the name Agrobacterium rosae sp. nov. is proposed. The type strain of A. rosae is NCPPB 1650T (=DSM 30203T=LMG 230T=CFBP 4470T=IAM 13558T=JCM 20915T).
Published: 2018

8. Tomato root microbiota and Phytophthora parasitica-associated disease

Author: Benoit Industri, Corinne Rancurel, Marie Larousse, Catherine Etienne, Xavier Nesme, Eric Galiana, Camille Syska, Ferran Palero, Marc Bardin, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Consejo Superior de Investigaciones Científicas, UMR 1355 ISA Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis (UNSA), Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), 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), Station de Pathologie Végétale (AVI-PATHO), Galiana, Eric, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), 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), Unité de Pathologie Végétale (PV), Institut Sophia Agrobiotech [Sophia Antipolis] ( ISA ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut National de la Recherche Agronomique ( INRA ), Université de Nice - Sophia Antipolis ( UNSA ), Institut National de la Recherche Agronomique ( INRA ), 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 Station de Pathologie Végétale ( AVI-PATHO )
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, champignon phytopathogène, tomato, Plant Roots, biofilm, tomate, Oomycete, Solanum lycopersicum, host plant, Gene Expression Regulation, Plant, diversité microbienne, RNA, Ribosomal, 16S, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, pathologie végétale, Phylogeny, [ SDV.MP.MYC ] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, Rhizosphere, biology, Microbiota, Pseudomonas, High-Throughput Nucleotide Sequencing, food and beverages, phytopathogenic fungus, 3. Good health, Agricultural sciences, Mycologie, lcsh:QR100-130, Pseudomonadaceae, Proteobacteria, Metagenomics 16S, rhizosphère, Flavobacteriaceae, phytophthora parasitica, Microbiology (medical), DNA, Bacterial, Phytophthora, 030106 microbiology, Virulence, Mycology, interaction microbienne, Microbiology, DNA, Ribosomal, lcsh:Microbial ecology, metagenomics 16S, 03 medical and health sciences, Microbial ecology, microbiote, Symbiosis, Host plant, Plant Diseases, Bacteria, Host (biology), Research, fungi, Bacteroidetes, Sequence Analysis, DNA, biology.organism_classification, pseudomonas, 030104 developmental biology, Biofilms, champignon du sol, Sciences agricoles
Abstract: Este artículo contiene 11 páginas, 6 figuras., Background: Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica. Results: Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P. parasitica biofilm. Colonization of the host root surface by the oomycete was associated with a shift in microbial community involving a Bacteroidetes/Proteobacteria transition and Flavobacteriaceae as the most abundant family. Identification of members of the P. parasitica-associated microbiota interfering with biology and oomycete infection was carried out by screening for bacteria able to (i) grow on a P. parasitica extract-based medium (ii), exhibit in vitro probiotic or antibiotic activity towards the oomycete (iii), have an impact on the oomycete infection cycle in a tripartite interaction S. lycopersicum-P. parasitica-bacteria. One Pseudomonas phylotype was found to exacerbate disease symptoms in tomato plants. The lack of significant gene expression response of P. parasitica effectors to Pseudomonas suggested that the increase in plant susceptibility was not associated with an increase in virulence. Our results reveal that Pseudomonas spp. establishes commensal interactions with the oomycete. Bacteria preferentially colonize the surface of the biofilm rather than the roots, so that they can infect plant cells without any apparent infection of P. parasitica. Conclusions: The presence of the pathogenic oomycete P. parasitica in the tomato rhizosphere leads to a shift in the rhizospheric microbiota composition. It contributes to the habitat extension of Pseudomonas species mediated through a physical association between the oomycete and the bacteria., This work was supported by a 3-year grant to Marie Larousse funded by INRA and the PACA region (France), and by a 1-year ATER position funded by the University of Nice Sophia Antipolis. Ferran Palero acknowledges a post-doctoral contract funded by the Beatriu de Pinos Programme of the Generalitat de Catalunya.
Published: 2017

9. Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR

Author: Malek Shams, C. Lavire, David Chapulliot, Xavier Nesme, Ludovic Vial, 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), EcoGenome project of Agence Nationale de la Recherche [ANR-08-BLAN-0090], CNRS contract in the framework of EcoGenome, 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: Rhizobiaceae, Agrobacterium, [SDV]Life Sciences [q-bio], Population, Biology, Rhizobacteria, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, Microbiology, law.invention, 03 medical and health sciences, law, education, Bacterial microdiversity, Soil Microbiology, Species identification, Ecology, Evolution, Behavior and Systematics, Polymerase chain reaction, DNA Primers, 030304 developmental biology, Genetics, Bacteriological Techniques, 0303 health sciences, education.field_of_study, 030306 microbiology, Agrobacterium tumefaciens, Plants, 15. Life on land, Amplicon, biology.organism_classification, Biota, Rec A Recombinases, PCR detection, Soil microbiology
Abstract: International audience; Abstract Agrobacteria are common soil bacteria that interact with plants as commensals, plant growth promoting rhizobacteria or alternatively as pathogens. Indigenous agrobacterial populations are composites, generally with several species and/or genomic species and several strains per species. We thus developed a recA-based PCR approach to accurately identify and specifically detect agrobacteria at various taxonomic levels. Specific primers were designed for all species and/or genomic species of Agrobacterium presently known, including 11 genomic species of the Agrobacterium tumefaciens complex (G1-G9, G13 and G14, among which only G2, G4, G8 and G14 still received a Latin epithet: pusense, radiobacter, fabrum and nepotum, respectively), A. larrymoorei, A. rubi, R. skierniewicense, A. sp. 1650, and A. vitis, and for the close relative Allorhizobium undicola. Specific primers were also designed for superior taxa, Agrobacterium spp. and Rhizobiaceace. Primer specificities were assessed with target and non-target pure culture DNAs as well as with DNAs extracted from composite agrobacterial communities. In addition, we showed that the amplicon cloning-sequencing approach used with Agrobacterium-specific or Rhizobiaceae-specific primers is a way to assess the agrobacterial diversity of an indigenous agrobacterial population. Hence, the agrobacterium-specific primers designed in the present study enabled the first accurate and rapid identification of all species and/or genomic species of Agrobacterium, as well as their direct detection in environmental samples.
Published: 2013

10. 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

11. Natural transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred

Author: Xavier Nesme, Franck Bertolla, Fanny Chaumeille-Dole, Pascal Simonet, Philippe Prior, BÃ©nÃ©dicte Coupat, and Saliou Fall
Subjects: 0303 health sciences, Species complex, Ralstonia solanacearum, Ecology, 030306 microbiology, Genetic transfer, food and beverages, Biology, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Transformation (genetics), genomic DNA, Plasmid, chemistry, Exogenous DNA, DNA, 030304 developmental biology
Abstract: Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA. We tested the ubiquity and variability of natural transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during natural transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the natural transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.
Published: 2008

12. GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Author: Laurent Duret, Thomas Bataillon, Séverine Périan, Vincent Daubin, Florent Lassalle, Xavier Nesme, 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), École normale supérieure - Lyon (ENS Lyon), Université de Lyon, 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), Bioinformatics Research Center, Aarhus University [Aarhus], 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), ANR [ANR-10-BINF-01-01 BLAN-08-0090], Ecole Normale Superieure de Lyon, ERC [BIG_IDEA 260801], 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), École normale supérieure de Lyon (ENS de Lyon), 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), 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 ), École normale supérieure - Lyon ( ENS Lyon ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: lcsh:QH426-470, Biodiversité et Ecologie, Gene Conversion, Bacterial genome size, Biology, Genome, Biodiversity and Ecology, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Genetic drift, génome bactérien, Databases, Genetic, Humans, Gene conversion, Selection, Genetic, Selection (genetic algorithm), 030304 developmental biology, base de données, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Base Composition, base nucléotidique, sélection génétique, Natural selection, Recombinant Proteins, lcsh:Genetics, conversion génique, Evolutionary biology, Codon usage bias, protéine recombinante, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery, GC-content, Genome, Bacterial, Research Article
Abstract: The characterization of functional elements in genomes relies on the identification of the footprints of natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures of selection. In mammals, and probably in many eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates patterns identical to what is expected under selection for higher GC-content, specifically in highly recombining genomic regions. Recent results have suggested that a mysterious selective force favouring higher GC-content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here, we show that gBGC is probably at work in most if not all bacterial species. First we find a consistent positive relationship between the GC-content of a gene and evidence of intra-genic recombination throughout a broad spectrum of bacterial clades. Second, we show that the evolutionary force responsible for this pattern is acting independently from selection on codon usage, and could potentially interfere with selection in favor of optimal AU-ending codons. A comparison with data from human populations shows that the intensity of gBGC in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is not restricted to sexual Eukaryotes but also widespread among Bacteria and could therefore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria, it can account for previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Because gBGC produces patterns similar to positive selection, it is essential to take this process into account when studying the evolutionary forces at work in bacterial genomes., Author Summary Classical population genetics models indicate that the efficiency of selection, and hence adaptation, depends on a number of non-selective factors, such as the size of a population or the intensity of recombination. In the last 10 years, evidence has accumulated that another mechanism called GC-Biased Gene Conversion (gBGC) can interfere with selection and even mimic its effects. This phenomenon, which arises from a particularity of the recombination machinery, was first thought to be restricted to sexual eukaryotic organisms. Here, we show that this mechanism probably exists in Bacteria and has a strong impact on their genome evolution. This discovery not only explains many previously unconnected features of bacterial genome evolution, but also highlights the importance of non-adaptive evolutionary processes in Bacteria.
Published: 2015

13. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology

Author: George M. Garrity, Jean Swings, Wilhelm Frederiksen, Erko Stackebrandt, Xavier Nesme, Martin C. J. Maiden, Alan C. Ward, Ramon Rosselló-Móra, Patrick A. D. Grimont, Luc Vauterin, William B. Whitman, Peter Kämpfer, Hans G Trüper, 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), 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, Bacterial, Societies, Scientific, 0303 health sciences, Bacteria, 030306 microbiology, [SDV]Life Sciences [q-bio], MEDLINE, Library science, Bacteriology, General Medicine, Biology, Bioinformatics, Microbiology, Bacterial Typing Techniques, 03 medical and health sciences, Bacterial Proteins, Species Specificity, Terminology as Topic, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: International audience; An ad hoc committee for the re-evaluation of the species definition in bacteriology met in Gent, Belgium, in February 2002. The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists.
Published: 2002

14. 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

15. Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid

Author: Vincent Daubin, Martha Helena Ramírez-Bahena, Ludovic Vial, Daniel Muller, Florent Lassalle, Xavier Nesme, Benjamin Diel, David Chapulliot, 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), 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), 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), 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 ), 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, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Rhizobiaceae, Genetic Speciation, Agrobacterium, Biovar, [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Genome, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Bacterial speciation, Evolution, Molecular, 03 medical and health sciences, Species complex, Genome architecture, TelA, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Clade, Telomerase, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Whole genome sequencing, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Base Sequence, biology, 030306 microbiology, Protelomerase, Chromosomes, Bacterial, biology.organism_classification, Rhizobium rhizogenes, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Rhizobium, Genome, Bacterial
Abstract: International audience; Linear chromosomes are atypical in bacteria and likely a secondary trait derived from ancestral circular molecules. Within the Rhizobiaceae family, whose genome contains at least two chromosomes, a particularity of Agrobacterium fabrum (formerly A. tumefaciens) secondary chromosome (chromid) is to be linear and hairpin-ended thanks to the TelA protelomerase. Linear topology and telA distributions within this bacterial family was screened by pulse field gel electrophoresis and PCR. In A. rubi, A. larrymoorei, Rhizobium skierniewicense, A. viscosum, Agrobacterium sp. NCPPB 1650, and every genomospecies of the biovar 1/A. tumefaciens species complex (including R. pusense, A. radiobacter, A. fabrum, R. nepotum plus seven other unnamed genomospecies), linear chromid topologies were retrieved concomitantly with telA presence, whereas the remote species A. vitis, Allorhizobium undicola, Rhizobium rhizogenes and Ensifer meliloti harbored a circular chromid as well as no telA gene. Moreover, the telA phylogeny is congruent with that of recA used as a marker gene of the Agrobacterium phylogeny. Collectively, these findings strongly suggest that single acquisition of telA by an ancestor was the founding event of a large and diverse clade characterized by the presence of a linear chromid. This clade, characterized by unusual genome architecture, appears to be a relevant candidate to serve as a basis for a possible redefinition of the controversial Agrobacterium genus. In this respect, investigating telA in sequenced genomes allows to both ascertain the place of concerned strains into Agrobacterium spp. and their actual assignation to species/genomospecies in this genus.
Published: 2014

16. IS292: a novel insertion element from Agrobacterium

Author: Cécile Ponsonnet, Gilles Pilate, Xavier Nesme, Philippe Normand, ProdInra, Migration, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), and Institut National de la Recherche Agronomique (INRA)
Subjects: DNA, Bacterial, Transposable element, Rhizobiaceae, Agrobacterium, Molecular Sequence Data, Restriction Mapping, Biology, medicine.disease_cause, Microbiology, Rhizobium leguminosarum, 03 medical and health sciences, Bacterial Proteins, Species Specificity, medicine, Direct repeat, Amino Acid Sequence, Insertion sequence, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, DNA Primers, 030304 developmental biology, Genetics, 0303 health sciences, Base Sequence, Sequence Homology, Amino Acid, 030306 microbiology, DNA–DNA hybridization, fungi, Nucleic acid sequence, food and beverages, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genes, Bacterial, DNA Transposable Elements, bacteria, Rhizobium
Abstract: A new insertion sequence, IS292, located in the 6b gene of a nopaline-type Agrobacterium strain (X88-292) isolated from poplar was identified and sequenced. IS292 is 2494 bp long, has 21 bp inverted terminal repeats with two mismatches, and generates 10 bp direct repeats upon integration. No sequence similarity was found between IS292 and other insertion elements associated with Agrobacterium, but it shows strong similarity with ISR/1 from Rhizobium leguminosarum bv. viciae. The occurrence of IS292-like sequences in various Agrobacterium isolates, especially different Agrobacterium strains isolated from the same biotope, was demonstrated by DNA hybridization.
Published: 1995

17. 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

18. Rapid and simultaneous detection of linear chromosome and large plasmids in Proteobacteria

Author: Martha Helena Ramírez-Bahena, Daniel Muller, Xavier Nesme, 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), ANR EcoGenome, Inra, 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), Ecologie microbienne ( EM ), 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 ( VAS )
Subjects: DNA, Bacterial, Genome evolution, Lineage (evolution), Bacterial genome size, Biology, Applied Microbiology and Biotechnology, Genome, Bacterial genetics, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Proteobacteria, Genome architecture, Pulsed Field Gel Electrophoresis (PFGE), Chromid, 030304 developmental biology, Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, 030306 microbiology, Chromosome, General Medicine, Chromosomes, Bacterial, Electrophoresis, Gel, Pulsed-Field, chemistry, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial, DNA, Plasmids
Abstract: International audience; Bacterial genomic architectures are complex and play important roles in genome evolution. While most bacterial lineage genomes contain a single chromosome often accompanied by plasmids, more and more genomes are described as harboring a linear or a second chromosome. Thus, the development of bacterial genomics leads to the study of bacterial genome architectures. In order to avoid laborious techniques combining several methods, we developed an original plug-free pulsed field gel electrophoresis procedure, that enabled us to co-characterize reproducibly the presence of linear chromosomes and plasmids ranging between 30 kb and 2000 kb in various proteobacterial lineages
Published: 2012

19. Bacillus subtilis bacteriocin Bac 14B with a broad inhibitory spectrum: Purification, amino acid sequence analysis, and physicochemical characterization

Author: Ali Rhouma, Ahmed Rebai, Abir Ben Bacha, Xavier Nesme, Bassem Jaouadi, Ines Hammami, Samir Bejar, Université de Sfax, Institut de l'Olivier, Ecologie Mircobienne, Institut National de la Recherche Agronomique (INRA), Tunisian Ministry of Higher Education and Scientific Research, 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), Lyon 1, Depot 1, 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: [SDV]Life Sciences [q-bio], Damping off, Alternaria solani, Biomedical Engineering, Bioengineering, bacteriolytical mode of action, Bacillus subtilis, Biology, Applied Microbiology and Biotechnology, Microbiology, Sepharose, 03 medical and health sciences, Bacteriocin, bacteriocin, COAGULANS, THURINGIENSIS, MALDI-TOF MS, MODE, Peptide sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, PLANT-PATHOGENS, Molecular mass, 030306 microbiology, STRAINS, food and beverages, biology.organism_classification, amino acid sequence, Bac 14B, [SDV] Life Sciences [q-bio], BIOCONTROL, Biochemistry, Shoot, BIOLOGICAL-CONTROL, Biotechnology
Abstract: International audience; Bacillus subtilis strain 14B was used to produce a novel antimicrobial peptide (bacteriocin) called Bac 14B. Pure bacteriocin was obtained after heat and acidic treatments (80A degrees C and pH 4), precipitation by ammonium sulfate, and chromatography on Sephadex G-50 and Mono Q Sepharose columns. Based on MALDI-TOF mass spectrometry analysis, purified Bac 14B is a monomer protein with a molecular mass of 20110.13 Da. N-terminal sequencing allowed for the straightforward identification of its first 12 residues, which were of a pure bacteriocin. It also revealed that this bacteriocin contained a unique sequence, namely M-L-K-A-N-L-Q-N-P-L-N-A, suggesting the identification of a novel compound. Bac 14B was stable for 1 h at temperatures up to 80A degrees C and pH of 4 similar to 8. It also proved sensitive to various proteases, which demonstrated its protein nature. Bac 14B displayed a bacteriolytical mode of action and a broad range of inhibitory spectra toward Gram-positive and -negative pathogens. Interestingly, based on conventional agronomic seed vigor parameters, the application of Bac 14B (500 activity units/mL) to various crops revealed that this bacteriocin was a potent exogenous enhancer of growth that stimulated the seedling vigor of tomatoes and muskmelons. Compared to those of the control, the germination percentage, shoot weight, shoot height, and root length were all significantly enhanced in Bac 14B-treated plant seeds. Bac 14B also exhibited effective disinfectant properties against a wide range of seedborne diseases and significant effects on the control of damping off diseases, particularly at the pregermination stage. It also proved to be effective against root rot diseases caused by Alternaria solani and other bacterial seedborne pathogens such as wilt diseases. The findings indicate that Bac 14B is the first B. subtilis-produced bacteriocin ever reported to exhibit such promising biological properties.
Published: 2012

20. 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

21. Ralstonia solanacearum Virulence Increased Following Large Interstrain Gene Transfers by Natural Transformation

Author: Franck Bertolla, Bénédicte Coupat-Goutaland, Dominique Bernillon, Xavier Nesme, Philippe Prior, Alice Guidot, 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), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), 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: Physiology, [SDV]Life Sciences [q-bio], Polymerase Chain Reaction, law.invention, PSEUDOMONAS-SOLANACEARUM, RALSTONIA SOLANACEARUM, FRENCH-WEST-INDIES, Solanum lycopersicum, law, Polymerase chain reaction, Phylogeny, Oligonucleotide Array Sequence Analysis, Phylotype, Genetics, 0303 health sciences, Ralstonia solanacearum, Comparative Genomic Hybridization, biology, Virulence, Genetic transfer, food and beverages, General Medicine, Horizontal gene transfer, BACTERIA, Plasmids, DNA, Bacterial, EXPRESSION, Gene Transfer, Horizontal, III EFFECTOR PROTEINS, SEQUENCE, Microbiology, Evolution, Molecular, 03 medical and health sciences, Transformation, Genetic, Gene, 030304 developmental biology, 030306 microbiology, STRAINS, Genetic Variation, Sequence Analysis, DNA, DNA, GENETIQUE, biology.organism_classification, genomic DNA, Genes, Bacterial, HYBRIDATION COMPARATIVE DU GENOME, Agronomy and Crop Science, Genome, Bacterial, SYSTEM
Abstract: International audience; Horizontal gene transfer (HGT) is a major driving force of evolution and is also likely to play an important role in the threatening emergence of novel pathogens, especially if it involves distantly related strains with substantially different pathogenicity. In this study, the impact of natural transformation on pathogenicity in six strains belonging to the four phylotypes of the plant-pathogenic bacterium Ralstonia solanacearum was investigated. The study focused on genomic regions that vary between donor and recipient strains and that carry genes involved in pathogenicity such as type III effectors. First, strains from R. solanacearum species complex were naturally transformed with heterologous genomic DNA. Transferred DNA regions were then determined by comparative genomic hybridization and polymerase chain reaction sequencing. We identified three transformant strains that acquired large DNA regions of up to 80 kb. In one case, strain Psi07 (phylotype IV tomato isolate) acquired 39.4 kb from GMI1000 (phylotype I tomato isolate). Investigations revealed that i) 24.4 kb of the acquired region contained 20 new genes, ii) an allelic exchange of 12 genes occurred, and iii) 27 genes (33.4 kb) formerly present in Psi07 were lost. Virulence tests with the three transformants revealed a significantincrease in the aggressiveness of BCG20 over its Psi07 parent on tomato. These findings demonstrate the potential importance of HGT in the pathogenic evolution of R. solanacearum strains and open new avenues for studying pathogen emergence.
Published: 2011

22. Première observation de la maladie de la galle du collet causée par Agrobacterium tumefaciens sur l'olivier en Tunisie

Author: Mehdi El Arbi, Ali Rhouma, Anissa Chaari, Xavier Nesme, 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), 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: 2. Zero hunger, 0106 biological sciences, 0303 health sciences, biology, 030306 microbiology, Agrobacterium, Inoculation, [SDV]Life Sciences [q-bio], Plant Science, Agrobacterium tumefaciens, biology.organism_classification, 01 natural sciences, Olive trees, Indicator plant, 03 medical and health sciences, Olea, Botany, GALLE DU COLLET, Gall, OLIVIER, Cultivar, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Abstract We observed for the first time crown gall symptoms in an orchard of olive trees (Olea europaea) of the variety \textquoteleftChemlali\textquoteright \textendash the most widely grown cultivar in Tunisia \textendash in the governorate of Kairouan in central Tunisia. Isolations from symptomatic tissues yielded bacteria that were identified as members of the species complex Agrobacterium tumefaciens using molecular techniques. The isolates were then evaluated for their pathogenicity by inoculating the indicator plant Kalankoë daigremontiana. The virulence of three isolates (O7, O9 and O11) was assessed by PCR amplification of part of the vir region of the Ti-plasmid of Agrobacterium and further confirmed for the O7 isolate by inducing the formation of tumours on \textquoteleftChemlali\textquoteright olive seedlings. These results confirm the susceptibility of the olive tree to Agrobacterium tumefaciens, as previously reported by other researchers in Algeria, Jordan, Australia and Argentina.
Published: 2011

23. Genomospecies identification and phylogenomic relevance of AFLP analysis of isolated and non-isolated strains of Frankia spp

Author: Xavier Nesme, M. Valdés, Maria P. Fernandez, G.H.H. Bautista, H.A. Cruz, H.A. Mendoza, 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), 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 Politecnico Nacional [Mexico] (IPN), CONACYT (48044), Mexico-France, and French Region Rhone-Alpes
Subjects: DNA, Bacterial, AFLP, [SDV]Life Sciences [q-bio], Frankia, Biology, Subspecies, EVOLUTIONARY GENOMIC DISTANCE, Applied Microbiology and Biotechnology, Microbiology, Genome, Polymerase Chain Reaction, 03 medical and health sciences, Magnoliopsida, Species Specificity, Phylogenetics, FRANKIA PHYLOGENY, Botany, Amplified Fragment Length Polymorphism Analysis, ADN BACTERIEN, Symbiosis, Genome size, Ecology, Evolution, Behavior and Systematics, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Frankia alni, 0303 health sciences, DISTANCE GENETIQUE, Phylogenetic tree, 030306 microbiology, GENOMOSPECIES, Genetic Variation, biology.organism_classification, UNCULTURED STRAINS, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, POLYMORPHISME DE LONGUEUR DE FRAGMENTS AMPLIFIES, Amplified fragment length polymorphism, HYBRIDATION DNA, Root Nodules, Plant, Genome, Bacterial
Abstract: Amplified fragment length polymorphism (AFLP) was tested as an alternative to the DNA-DNA hybridization technique (DDH) to delineate genomospecies and the phylogenetic structure within the genus Frankia. Forty Frankia strains, including representatives of seven DDH genomospecies, were typed in order to infer current genome mispairing (CGM) and evolutionary genomic distance (EGD). The constructed phylogeny revealed the presence of three main clusters corresponding to the previously identified host-infecting groups. In all instances, strains previously assigned to the same genomospecies were grouped in coherent clusters. A highly significant correlation was found between DDH values and CGM computed from AFLP data. The species definition threshold was found to range from 0.071 to 0.098 mismatches per site, according to host-infecting groups, presumably as a result of large genome size differences. Genomic distances allowed new Frankia strains to be assigned to nine genomospecies previously determined by DDH. The applicability of AFLP for the characterization of uncultured endophytic strains was tested on experimentally inoculated plants and then applied to Alnus incana and A. viridis field nodules hosting culture refractory spore-positive (Sp+, that sporulate in planta) strains. Only 1.3% of all AFLP fragments were shown to be generated by the contaminant plant DNA and did not interfere with accurate genomospecies identification of strains. When applied to field nodules, the procedure revealed that Alnus Sp+ strains were bona fide members of the Alnus-Myrica host infecting group. They displayed significant genomic divergence from genomospecies G1 of Alnus infecting strains (i.e. Frankia alni) and thus may belong to another subspecies or genomospecies. (C) 2011 Elsevier GmbH. All rights reserved.
Published: 2011

24. 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

25. Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas

Author: Olivier Pruvost, Xavier Nesme, Nathalie Ah-You, Pierre Lefeuvre, Christian Vernière, L. Bui Thi Ngoc, Frédéric Chiroleu, Emmanuel Jouen, Sylvain Brisse, Lionel Gagnevin, Patrick A. D. Grimont, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Biodiversité des Bactéries Pathogènes Émergentes, Institut Pasteur [Paris], 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), Institut Pasteur [Paris] (IP), 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), UMR Peuplements végétaux et bioagresseurs en milieu tropical ( UMR PVBMT - Université de La Réunion ), Université de la Réunion ( UR ), 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 ), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (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: MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, Xanthomonas citri, RNA, Ribosomal, 16S, Genotype, Anacardiaceae, MESH: Genetic Variation, Amplified Fragment Length Polymorphism Analysis, MESH: Phylogeny, Phylogeny, 0303 health sciences, biology, Phylogenetic tree, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, General Medicine, MESH: RNA, Ribosomal, 16S, Pathovar, Sequence Analysis, 16S, Xanthomonas, Molecular Sequence Data, MESH: Amplified Fragment Length Polymorphism Analysis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, MESH: Xanthomonas, Microbiology, 03 medical and health sciences, MESH : Xanthomonas, Phylogenetics, MESH : Genetic Variation, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, H20 - Maladies des plantes, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, Ribosomal, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, MESH: Molecular Sequence Data, MESH : Anacardiaceae, 030306 microbiology, MESH : Amplified Fragment Length Polymorphism Analysis, MESH : Phylogeny, Genetic Variation, Sequence Analysis, DNA, DNA, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, MESH : RNA, Ribosomal, 16S, MESH: Anacardiaceae, RNA, Amplified fragment length polymorphism, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MESH : Sequence Analysis, DNA
Abstract: International audience; We have used amplified fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and DNA-DNA hybridization for genotypic classification of Xanthomonas pathovars associated with the plant family Anacardiaceae. AFLP and MLSA results showed congruent phylogenetic relationships of the pathovar mangiferaeindicae (responsible for mango bacterial canker) with strains of Xanthomonas axonopodis subgroup 9.5. This subgroup includes X. axonopodis pv. citri (synonym Xanthomonas citri). Similarly, the pathovar anacardii, which causes cashew bacterial spot in Brazil, was included in X. axonopodis subgroup 9.6 (synonym Xanthomonas fuscans). Based on the thermal stability of DNA reassociation, consistent with the AFLP and MLSA data, the two pathovars share a level of similarity consistent with their being members of the same species. The recent proposal to elevate X. axonopodis pv. citri to species level as X. citri is supported by our data. Therefore, the causal agents of mango bacterial canker and cashew bacterial spot should be classified as pathovars of X. citri, namely X. citri pv. mangiferaeindicae (pathotype strain CFBP 1716) and X. citri pv. anacardii (pathotype strain CFBP 2913), respectively. Xanthomonas fuscans should be considered to be a later heterotypic synonym of Xanthomonas citri.
Published: 2009

26. Homologous Recombination in Agrobacterium: Potential Implications for the Genomic Species Concept in Bacteria

Author: Franck Bertolla, Denis Costechareyre, Xavier Nesme, 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), 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), Ecologie microbienne ( EM ), 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 ( VAS )
Subjects: Species complex, Genetic Speciation, Agrobacterium, homologous recombination, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Genetic recombination, Genome, Gene flow, 03 medical and health sciences, sexual isolation, Genetics, bacterial species, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, Recombination, Genetic, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Concerted evolution, Bacteria, 030306 microbiology, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Homologous recombination, Genome, Bacterial, Recombination, Rhizobium
Abstract: International audience; According to current taxonomical rules, a bona fide bacterial species is a genomic species characterized by the genomic similarity of its members. It has been proposed that the genomic cohesion of such clusters may be related to sexual isolation, which limits gene flow between too divergent bacteria. Homologous recombination is one of the most studied mechanisms responsible for this genetic isolation. Previous studies on several bacterial models showed that recombination frequencies decreased exponentially with increasing DNA sequence divergence. In the present study, we investigated this relationship in the Agrobacterium tumefaciens species complex, which allowed us to focus on sequence divergence in the vicinity of the genetic boundaries of genomic species. We observed that the sensitivity of the recombination frequency to DNA divergence fitted a log-linear function until approximately 10% sequence divergence. The results clearly revealed that there was no sharp drop in recombination frequencies at the point where the sequence divergence distribution showed a ‘‘gap'' delineating genomic species. The ratio of the recombination frequency in homogamic conditions relative to this frequency in heterogamic conditions, that is, sexual isolation, was found to decrease from 8 between the most distant strains within a species to 9 between the most closely related species, for respective increases from 4.3% to 6.4% mismatches in the marker gene chvA. This means that there was only a 1.13-fold decrease in recombination frequencies for recombination events at both edges of the species border. Hence, from the findings of this investigation, we conclude that—at least in this taxon—sexual isolation based on homologous recombination is likely not high enough to strongly hamper gene flow between species as compared with gene flow between distantly related members of the same species. The 70% relative binding ratio cutoff used to define bacterial species is likely correlated to only minor declines in homologous recombination frequencies. Consequently, the sequence diversity, as a mechanistic factor for the efficiency of recombination (as assayed in the laboratory), appears to play little role in the genetic cohesion of bacterial species, and thus, the genomic species definition for prokaryotes is definitively not reconcilable with the biological species concept for eukaryotes.
Published: 2009

27. Optimization and biochemical characterization of a bacteriocin from a newly isolated Bacillus subtilis strain 14B for biocontrol of Agrobacterium spp. strains

Author: Ines Hammami, Ali Rhouma, Ahmed Rebai, Bassem Jaouadi, Xavier Nesme, Unite de Bioinformatique, Centre de Biotechnologie de Sfax (CBS), Unite de Recherche Protection des Plantes Cultivees et Environnement (URPPC), Institut de l'Olivier, Laboratoire d'Enzymes et de Metabolites des Procaryotes (LEMP), 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), Tunisian Government 'Ministere de l'Enseignement SupErieur, de la Recherche Scientifique et de la Technologie', Centre de Biotechnologie de Sfax ( CBS ), 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: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Agrobacterium, Molecular Sequence Data, Bacillus subtilis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Bacteriocin, Bacteriocins, Solanum lycopersicum, bacteriocin, Plant Tumors, Gall, biocontrol, 030304 developmental biology, 2. Zero hunger, Gel electrophoresis, optimization, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, Strain (chemistry), 030306 microbiology, Protein Stability, fungi, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, food and beverages, Agrobacterium tumefaciens, biology.organism_classification, Antimicrobial, Anti-Bacterial Agents, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Molecular Weight, bacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Aims: The identification of a new compound active against Agrobacterium tumefaciens. Methods and Results: The culture conditions of a newly isolated Bacillus subtilis strain, designed 14B, were optimized, as a first step, to produce its bacteriocin (termed Bac 14B) for the biocontrol of Agrobacterium spp., the causal agents of the crown gall disease. Bac 14B was then partially purified and biochemically characterized. Bacillus subtilis 14B was observed to produce an antibacterial compound having a protinaceous nature. As estimated by sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE), the semi-purified bacteriocin substance was found to be a monomeric protein with a molecular weight of 21 kDa. While the latter's antimicrobial activity was completely stable during exposure to a temperature range of up to 100C for 2 h, its initial activity was totally lost at 121C for 20 min. The maximum bacteriocin production (4096 AU ml)1) was recorded after 96 h-incubation in an optimized Luria Bertani medium supplemented with 10 g l)1 glucose, 15 g l)1 K2HPO4 and 5 g l)1 MgSO4 7H2O at 30C in a shaking flask culture. Interestingly, the B. subtilis 14B culture supernatant that contained the bacteriocin under study was proved efficient in reducing both the percentage of galled plants and the number of galls in tomato. Conclusion: The findings revealed that B. subtilis 14B and its bacteriocin are efficient in reducing the percentage of infections in plants caused by Ag. tumefaciens. Significance and Impact of the Study: The results could be useful for the nurserymen who are particularly interested in the biocontrol of the crown gall disease.
Published: 2009

28. Eucalyptus occidentalis plantlets are naturally infected by pathogenic Agrobacterium tumefaciens

Author: Zoulikha Krimi, Yves Dessaux, Xavier Nesme, Aida Raio, Annik Petit, Laboratoire de Phytobactériologie, Faculté des Sciences Agronomiques et Vétérinaires, Université de Saâd Dahlab [Blida] (USDB ), Instituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche [Roma] (CNR), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 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), Université de Blida, Consiglio Nazionale delle Ricerche [Roma] ( CNR ), Institut des sciences du végétal ( ISV ), 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 ), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, food.ingredient, Agrobacterium, Ti plasmid, agrocin 84 : opine, Opine, Plant Science, Horticulture, Biology, 01 natural sciences, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, food, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 16S rRNA, 0303 health sciences, 030306 microbiology, Eucalyptus occidentalis, Agrobacterium tumefaciens, 15. Life on land, biology.organism_classification, plant pathogen, Eucalyptus camaldulensis, chemistry, Chromosomal region, Nopaline, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: In the Sidi M'djahed nursery (Algeria), over 60,000 eucalyptus (Eucalyptus occidentalis) plantlets exhibited tumour-like growths localized at the crown of the plants that resembled crown galls caused by Agrobacterium tumefaciens. Bacteria colonizing the galls were isolated and purified. Most (22 out of 24) of the isolates had cultural and biochemical characteristics similar to those of strains of the biovar 1 of A. tumefaciens. Twenty out of 22 Agrobacterium isolates induced tumour formation on various test plants. In PCR experiments, DNA extracted from these virulent strains yielded an amplification signal corresponding to a 247-bp fragment located within the virulence region of nopaline type Ti plasmid. Consistent with this, the opine nopaline was detected in the tumours induced on test plants – but not on eucalyptus plants. Nopaline was degraded by the 20 pathogenic isolates that were also sensitive to agrocin 84, indicating the presence of a nopaline-type pTi in these strains. The chromosomal region encoding the 16S rRNA was analyzed in a sub-population of the pathogenic agrobacterial isolates. The analyzed strains were found to belong to the ribogroup of the reference strain B6. Interestingly, Eucalyptus camaldulensis and Eucalyptus cladocalyx grown in the same nursery and in the same soil substrate developed no galls.
Published: 2006

29. Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities

Author: Arnaud Dechesne, Geneviève L. Grundmann, Xavier Nesme, Timothy M. Vogel, Benoît Remenant, Hervé Sanguin, Jean Thioulouse, Yvan Moënne-Loccoz, Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], 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), Ampère, Département Bioingénierie (BioIng), Ampère, École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), 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)-École Centrale de Lyon (ECL), 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), 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), Technical University of Denmark [Lyngby] (DTU), Ampère (AMPERE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-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)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-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), 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), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université de Lyon, 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 ), École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), and Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: DIVERSITY, Polymerase Chain Reaction, Applied Microbiology and Biotechnology, [ SPI.NRJ ] Engineering Sciences [physics]/Electric power, RNA, Ribosomal, 16S, MICROBIAL COMMUNITIES, Cloning, Molecular, Phylogeny, Soil Microbiology, Oligonucleotide Array Sequence Analysis, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, 0303 health sciences, Rhizosphere, Ecology, biology, DNA MICROARRAYS, Planctomycetes, RNA, Bacterial, POPULATIONS, DNA microarray, Proteobacteria, Rhizobium, Biotechnology, GENES, Bulk soil, Zea mays, Microbial Ecology, Actinobacteria, ARN RIBOSOMIQUE 16S, 03 medical and health sciences, GRADIENT GEL-ELECTROPHORESIS, Botany, TAXANOMIE, WOLBACHIA-PIPIENTIS, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, TARGETED OLIGONUCLEOTIDE PROBES, 030306 microbiology, [SPI.NRJ]Engineering Sciences [physics]/Electric power, Verrucomicrobia, GENETIQUE, 15. Life on land, biology.organism_classification, SOIL BACTERIA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, BULK SOIL, Food Science, Acidobacteria
Abstract: Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria . Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria , Bacteroidetes , Verrucomicrobia , and Planctomycetes , a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae , and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.
Published: 2006

30. Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers

Author: Catherine Lerondelle, David Chapulliot, Jean Thioulouse, Perrine Portier, Xavier Nesme, Marion Fischer-Le Saux, Christophe Mougel, 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), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [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)-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), 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), Pathologie Végétale, Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Pathologie végétale et phytobactériologie, Institut National de la Recherche Agronomique (INRA), 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 d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ), 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 ), 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-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: Genetic Markers, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Agrobacterium, Biovar, Genomics, HYBRIDATION ADN-ADN, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, TAXONOMIE, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, Genome, 03 medical and health sciences, Species Specificity, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Methods, Environmental Microbiology, Humans, 030304 developmental biology, Genetics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Ecology, biology, 030306 microbiology, Strain (biology), Nucleic Acid Hybridization, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Agrobacterium tumefaciens, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacterial Typing Techniques, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetic marker, AGROBACTERIUM, Amplified fragment length polymorphism, Genome, Bacterial, Polymorphism, Restriction Fragment Length, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Food Science, Biotechnology, Rhizobium
Abstract: Biovar 1 of the genus Agrobacterium consists of at least nine genomic species that have not yet received accepted species names. However, rapid identification of these organisms in various biotopes is needed to elucidate crown gall epidemiology, as well as Agrobacterium ecology. For this purpose, the AFLP methodology provides rapid and unambiguous determination of the genomic species status of agrobacteria, as confirmed by additional DNA-DNA hybridizations. The AFLP method has been proven to be reliable and to eliminate the need for DNA-DNA hybridization. In addition, AFLP fragments common to all members of the three major genomic species of agrobacteria, genomic species G1 (reference strain, strain TT111), G4 (reference strain, strain B6, the type strain of Agrobacterium tumefaciens ), and G8 (reference strain, strain C58), have been identified, and these fragments facilitate analysis and show the applicability of the method. The maximal infraspecies current genome mispairing (CGM) value found for the biovar 1 taxon is 10.8%, while the smallest CGM value found for pairs of genomic species is 15.2%. This emphasizes the gap in the distribution of genome divergence values upon which the genomic species definition is based. The three main genomic species of agrobacteria in biovar 1 displayed high infraspecies current genome mispairing values (9 to 9.7%). The common fragments of a genomic species are thus likely “species-specific” markers tagging the core genomes of the species.
Published: 2006

31. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria

Author: Pascal Simonet, Geneviève L. Grundmann, Arnaud Dechesne, Yvan Moënne-Loccoz, Elisabeth Navarro, Xavier Nesme, Timothy M. Vogel, Christine Oger-Desfeux, Aude Herrera, Hervé Sanguin, 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 ), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS )
Subjects: Library, SEQUENÇAGE PAR OLIGONUCLEOTIDES EN BATTERIE, Molecular Sequence Data, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Computational biology, ARN BACTERIEN, Biology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Sensitivity and Specificity, Microbiology, law.invention, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [ SDV.SA.AGRO ] Life Sciences [q-bio]/Agricultural sciences/Agronomy, law, RNA, Ribosomal, 16S, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Taxonomic rank, Phylogeny, Ecology, Evolution, Behavior and Systematics, Polymerase chain reaction, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0303 health sciences, Base Sequence, 030306 microbiology, Microarray analysis techniques, Alphaproteobacteria, Ribosomal RNA, Amplicon, GENETIQUE, 16S ribosomal RNA, biology.organism_classification, Molecular biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [ SDV.EE.ECO ] Life Sciences [q-bio]/Ecology, environment/Ecosystems, RNA, Bacterial, ALPHAPROTEOBACTERIA, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria ). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM > 2 with target DNA displayed only 2.8% false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium -related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7% of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems
Published: 2006

32. Engineering root exudation of Lotus towards the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere

Author: Xavier Nesme, Yves Dessaux, Philippe Oger, H. Mansouri, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Sciences de la Terre (LST), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS 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), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Sciences de la Terre ( LST ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers ( INSU - CNRS ) -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 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.BV ] Life Sciences [q-bio]/Vegetal Biology, food.ingredient, Agrobacterium, Lotus, Sequence Homology, Soil Science, Opine, Biology, Arginine, Plant Roots, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, food, RNA, Ribosomal, 16S, Botany, Duganella, Cluster Analysis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Mannitol, Phyllobacterium, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Rhizosphere, Bacteria, Ecology, 030306 microbiology, fungi, Genetic Variation, food and beverages, Sequence Analysis, DNA, Agrobacterium tumefaciens, 15. Life on land, Plants, Genetically Modified, biology.organism_classification, chemistry, France, Nopaline, Polymorphism, Restriction Fragment Length
Abstract: The culture of opine-producing transgenic Lotus plants induces the increase in the rhizosphere of bacterial communities that are able to utilize these molecules as sole carbon source. We used transgenic Lotus plants producing two opines, namely mannopine and nopaline, to characterize the microbial communities directly influenced by the modification of root exudation. We showed that opine-utilizers represent a large community in the rhizosphere of opine-producing transgenic Lotus. This community is composed of at least 12 different bacterial species, one third of which are able to utilize the opine mannopine and two thirds the opine nopaline. Opine utilizers are diverse, belonging to the Gram-positive and -negative bacteria. We described two novel mannopine-utilizing species, Rhizobium and Duganella spp., and five novel nopaline-utilizing species, Duganella, Afipia, Phyllobacterium, Arthrobacter, and Bosea spp. Although opine utilizers mostly belong to the α-Proteobacteria, Rhizobiaceae family, there is little overlap between the populations able to utilize each of the two opines produced by the plants. Noticeably, in the rhizosphere of transgenic Lotus, only the opine mannopine favors the growth of Agrobacterium tumefaciens, the bacterium from which opines have been characterized. The diversity of opine utilizers from the rhizosphere of Lotus plants is greater than that observed from any other environment. Therefore, transgenic plants with engineered exudation constitute an excellent tool to isolate and characterize specific microbial populations.
Published: 2004

33. Chromosomal and plasmid diversity of Agrobacterium strains isolated from Ficus benjamina tumors

Author: Aida Raio, Astolfo Zoina, Raffaele Peluso, Xavier Nesme, 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-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), Raio, A., Peluso, R., Nesme, X., and Zoina, Astolfo
Subjects: Rhizobiaceae, Agrobacterium, Biovar, [SDV]Life Sciences [q-bio], Plant Science, Horticulture, Microbiology, 03 medical and health sciences, Ti plasmid, Plasmid, Genotype, plasmid profile, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, biology, 030306 microbiology, population structure, Ribosomal RNA, biology.organism_classification, ribotype, pTi, Restriction fragment length polymorphism, Agronomy and Crop Science, Agrobacterium larrymoorei
Abstract: Agrobacteria were previously isolated from tumors developing on branches and aerial and hypogeous roots of weeping fig plants in Italy and in The Netherlands. A representative group of 48 strains was analyzed by PCR– RFLP of 16S and 16S + IGS ribosomal regions, PCR–RFLP of six Ti plasmid (pTi) regions and characterized for plasmid content. Two groups of agrobacteria were separated by cluster analysis of PCR–RFLP profiles of rrs gene: seventeen strains were similar to the new species Agrobacterium larrymoorei, while the remaining strains were included within the agrobacterium biovar 1 group. Sixteen different plasmid profiles from one to five plasmids were observed. In addition, 21 ribotypes and 20 pTi structures were arranged in many different combinations, showing that fig agrobacteria were characterized by a wide heterogeneity. A general lack of correlation between strain ribotypes and plasmid content was observed.
Published: 2004

34. A highly selectable and highly transferable Ti plasmid to study conjugal host range and Ti plasmid dissemination in complex ecosystems

Author: Xavier Nesme, S. Teyssier-Cuvelle, Stephen K. Farrand, K. Groud, Christophe Mougel, Phil M. Oger, 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), Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, 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: Rhizobiaceae, food.ingredient, Agrobacterium, [SDV]Life Sciences [q-bio], DNA, Recombinant, Soil Science, Microbiology, 03 medical and health sciences, Ti plasmid, chemistry.chemical_compound, food, Plasmid, Species Specificity, Drug Resistance, Bacterial, Phyllobacterium, Plant Tumor-Inducing Plasmids, Ecology, Evolution, Behavior and Systematics, T-DNA Binary system, ComputingMilieux_MISCELLANEOUS, Ecosystem, 030304 developmental biology, 2. Zero hunger, Genetics, Octopine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, biology, 030306 microbiology, Chromosome Mapping, biology.organism_classification, chemistry, 13. Climate action, Conjugation, Genetic, Rhizobium
Abstract: A conjugal donor system, ST2, was constructed to study the conjugal dissemination of a Ti plasmid to wild-type recipient bacteria in vitro and in situ. The system consisted of a polyauxotrophic derivative of C58 harboring a hyperconjugative and highly selectable Ti plasmid, pSTiEGK, which was constructed by inserting a multiple antibiotic resistance cassette in the traM- mcpA region of pTiC58Delta accR. ST2 transfers pSTiEGK constitutively at frequencies up to 10(-1) to plasmidless Agrobacterium recipients. The host range of pSTiEGK includes all the known genomic species of Agrobacterium, indigenous soil agrobacteria and some Rhizobium and Phyllobacterium spp. All transconjugants became pathogenic upon acquisition of the Ti plasmid and were also able to transfer pSTiEGK by conjugation. This host range was indistinguishable from that of its wild-type parent pTiC58, and therefore pSTiEGK constitute a valid proxy to study the dissemination of Ti plasmids directly in the environment. Transconjugants can be selected on a combination of four antibiotics, which efficiently prevents the growth of the indigenous microbiota present in complex environments. The transfer of pSTiEGK to members of the genus Agrobacterium was affected primarily by the plasmid content of the recipient strain (10(3)- to 10(5)-fold reduction), e.g., the presence of incompatible plasmids. As a consequence, a species should be considered permissive to Ti transfer whenever one permissive isolate is found.
Published: 2003

35. Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil

Author: John P. Vogel, Geneviève L. Grundmann, Philippe Normand, Jean Thioulouse, Xavier Nesme, 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), 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), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [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)-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), 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: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Agrobacterium, Biovar, Population, Population Dynamics, Biology, Applied Microbiology and Biotechnology, Genetic analysis, Ribotyping, Zea mays, Microbial Ecology, 03 medical and health sciences, education, Ecosystem, Soil Microbiology, 030304 developmental biology, 0303 health sciences, education.field_of_study, Genetic diversity, Ecology, 030306 microbiology, Genetic Variation, Agriculture, biology.organism_classification, Amplified Ribosomal DNA Restriction Analysis, Taxon, Genetic distance, Evolutionary biology, Food Science, Biotechnology, Rhizobium
Abstract: The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 μm in diameter were sampled with spatial coordinates in 1 cm 3 of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10 3 agrobacteria g −1 ), a high genetic diversity was maintained. In two independent microsamples (500 μm in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.
Published: 2003

36. Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils

Author: Yves Dessaux, Zoulikha Krimi, Christophe Mougel, Xavier Nesme, Annik Petit, Département de Foresterie, Faculté des Sciences, Université de Tlemcen, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie ( PMEBBCE ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -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 ), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), 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), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-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 ProdInra, Migration
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Biovar, Applied Microbiology and Biotechnology, Polymerase Chain Reaction, Ti plasmid, chemistry.chemical_compound, Plant Microbiology, MESH : Ecosystem, MESH : DNA, Bacterial, MESH: Ecosystem, MESH : Polymerase Chain Reaction, ComputingMilieux_MISCELLANEOUS, Soil Microbiology, 2. Zero hunger, Octopine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Rhizosphere, education.field_of_study, Ecology, biology, Bacterial, Horticulture, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, POUVOIR PATHOGENE, Seasons, Soil microbiology, Biotechnology, Plasmids, Rhizobium, MESH: Rhizobium, DNA, Bacterial, Agrobacterium, Population, MESH : Soil Microbiology, Bulk soil, MESH : Rhizobium, 03 medical and health sciences, MESH: Plasmids, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Ecosystem, 030304 developmental biology, MESH : Seasons, 030306 microbiology, MESH: Polymerase Chain Reaction, DNA, biology.organism_classification, MESH: DNA, Bacterial, chemistry, MESH: Soil Microbiology, MESH : Plasmids, MESH: Seasons, Food Science
Abstract: Short- and long-term persistence of pathogenic (i.e., tumor forming) agrobacteria in soil was investigated in six nursery plots with a history of high crown gall incidence. No pathogenic Agrobacterium strains were isolated in soil samples taken in fall and winter in any plots, but such strains were isolated from both bulk soils and weed rhizospheres (over 0.5 × 10 5 pathogenic CFU/g of bulk soil or rhizosphere) in three out of six plots in spring and summer. PCR amplifications of a vir sequence from DNA extracted from soil confirmed the presence of Ti plasmids in summer and their absence in fall and winter. The results indicate that strains that harbor a Ti plasmid had an unforeseen positive fitness versus Ti plasmid-free strains in soil and rhizosphere in spring and summer in spite of the apparent absence of tumor, and hence of opines. The gain of fitness occurred during a bloom of all cultivable agrobacteria observed only in conducive soils. An evolution of the pathogenic population was recorded during a 4-year period in one particularly conducive soil. In 1990, the pathogenic population in this soil consisted of only biovar 1 strains harboring both octopine- and nopaline-type Ti plasmids. In 1994, it consisted of only nopaline-type Ti plasmids equally distributed among biovar 1 and 2 strains. These results suggest that nopaline-type Ti plasmids conferred a better survival ability than octopine-type Ti plasmids to biovar 2 agrobacteria under the present field conditions.
Published: 2002

37. Relationships between Staphylococcus aureus genetic background, virulence factors, agr groups (alleles), and human disease

Author: Hélène Meugnier, Françoise Forey, Jean Thioulouse, Jerome Etienne, Xavier Nesme, Sophie Jarraud, Gerard Lina, François Vandenesch, Christophe Mougel, ProdInra, Migration, 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), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [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)-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-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), Microbiologie, and Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)
Subjects: [SDE] Environmental Sciences, Staphylococcus aureus, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], [SDV]Life Sciences [q-bio], Bacterial Toxins, Immunology, Virulence, Locus (genetics), Biology, medicine.disease_cause, Microbiology, law.invention, 03 medical and health sciences, Bacterial Proteins, law, Phylogenetics, medicine, Humans, Allele, Peptide sequence, ComputingMilieux_MISCELLANEOUS, Alleles, Phylogeny, Polymerase chain reaction, 030304 developmental biology, Genetics, 0303 health sciences, 030306 microbiology, Bacterial Infections, Staphylococcal Infections, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, [SDV] Life Sciences [q-bio], Infectious Diseases, POUVOIR PATHOGENE, [SDE]Environmental Sciences, Trans-Activators, bacteria, Female, Parasitology, Amplified fragment length polymorphism, Signal Transduction
Abstract: The expression of most Staphylococcus aureus virulence factors is controlled by the agr locus, which encodes a two-component signaling pathway whose activating ligand is an agr -encoded autoinducing peptide (AIP). A polymorphism in the amino acid sequence of the AIP and of its corresponding receptor divides S. aureus strains into four major groups. Within a given group, each strain produces a peptide that can activate the agr response in the other member strains, whereas the AIPs belonging to different groups are usually mutually inhibitory. We investigated a possible relationship between agr groups and human S. aureus disease by studying 198 S. aureus strains isolated from 14 asymptomatic carriers, 66 patients with suppurative infection, and 114 patients with acute toxemia. The agr group and the distribution of 24 toxin genes were analyzed by PCR, and the genetic background was determined by means of amplified fragment length polymorphism (AFLP) analysis. The isolates were relatively evenly distributed among the four agr groups, with 61 strains belonging to agr group I, 49 belonging to group II, 43 belonging to group III, and 45 belonging to group IV. Principal coordinate analysis performed on the AFLP distance matrix divided the 198 strains into three main phylogenetic groups, AF1 corresponding to strains of agr group IV, AF2 corresponding to strains of agr groups I and II, and AF3 corresponding to strains of agr group III. This indicated that the agr type was linked to the genetic background. A relationship between genetic background, agr group, and disease type was observed for several toxin-mediated diseases: for instance, agr group IV strains were associated with generalized exfoliative syndromes, and phylogenetic group AF1 strains with bullous impetigo. Among the suppurative infections, endocarditis strains mainly belonged to phylogenetic group AF2 and agr groups I and II. While these results do not show a direct role of the agr type in the type of human disease caused by S. aureus , the agr group may reflect an ancient evolutionary division of S. aureus in terms of this species’ fundamental biology.
Published: 2002

38. Molecular tools for the characterisation of antibiotic-resistant bacteria

Author: Karim Sidi Boumedine, Henk J.M. Aarts, Xavier Nesme, Axel Cloeckaert, 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: New approaches, antibiotic resistance, Databases, Factual, Antibiotic resistance, nouvelles approches, Antibiotics, résistance aux antibiotiques, Molecular typing, détection moléculaire, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Molecular detection, typage moléculaire, 0303 health sciences, Strain (biology), [SDV.BA]Life Sciences [q-bio]/Animal biology, Strain typing, Drug Resistance, Microbial, Horizontal gene transfer, méthode de détection, molecular detection, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetic Techniques, horizontal gene transfer, [SDV.IMM]Life Sciences [q-bio]/Immunology, Veterinary medicine and animal Health, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Gene Transfer, Horizontal, medicine.drug_class, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, 03 medical and health sciences, new approaches, résistance aux antibiotiques, medicine, Gene, 030304 developmental biology, Bacteriological Techniques, General Veterinary, Bacteria, 030306 microbiology, business.industry, Mechanism (biology), Wageningen Food Safety Research, molecular typing, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biotechnology, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Médecine vétérinaire et santé animal, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, transfert horizontal de gènes
Abstract: International audience; This review will discuss a number of molecular tools which are currently used as well as some innovative approaches for the characterisation of antibiotic-resistant bacterial strains. Various methods involved in the detection and characterisation of genes and mutations associated with antibiotic resistance and that are used for strain typing as part of epidemiological studies, are described. Furthermore, a few examples are discussed in which the results of both gene and strain characterisation are combined to investigate the underlying mechanism of the spread of antibiotic resistance. Some of the available molecular techniques are heavily supported by the existence of databases on the Internet. These databases either contain a fast growing amount of sequence information or a large number of allelic or fingerprint profiles. The current progress in applied DNA technology and the ongoing projects on the elucidation of the whole genomic sequence of bacterial species have lead and will further lead to the development and application of sophisticated new strategies for the analysis of antibiotic resistant bacterial strains.; Outils moléculaires pour la caractérisation de bactéries résistantes aux antibiotiques. Cette revue présente les outils moléculaires utilisés actuellement ainsi que des nouvelles approches pour la caractérisation de souches bactériennes résistantes aux antibiotiques. Différentes méthodes de détection et de caractérisation des gènes et des mutations impliqués dans la résistance aux antibiotiques, utilisées dans des études épidémiologiques, sont décrites. Quelques exemples sont présentés où sont associées les caractérisations du gène et de la souche bactérienne dans l'étude des mécanismes de diffusion de résistances aux antibiotiques. Certaines techniques moléculaires font largement appel aux banques de données disponibles sur Internet. Ces banques de données contiennent un nombre croissant d'informations comprenant des séquences ou des profils de typages moléculaires. Le progrès fait actuellement au niveau de technologies ADN appliquées et les projets en cours sur les séquençages de génomes entiers des espèces bactériennes ont conduit et conduiront progressivement au développement et à l'application de nouvelles stratégies sophistiquées pour l'analyse de souches bactériennes résistantes aux antibiotiques.
Published: 2001

39. Plant Genome Complexity May Be a Factor Limiting In Situ the Transfer of Transgenic Plant Genes to the Phytopathogen Ralstonia solanacearum

Author: Xavier Nesme, Eric Paget, Eugenie Passelegue-Robe, Régis Pépin, Andrew J. Simkin, Pascal Simonet, Franck Bertolla, 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), 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: Transgene, [SDV]Life Sciences [q-bio], Genetically modified crops, Applied Microbiology and Biotechnology, Genome, Microbiology, 03 medical and health sciences, Plant Microbiology, Solanum lycopersicum, Transgenes, Gene, ComputingMilieux_MISCELLANEOUS, Plant Diseases, 030304 developmental biology, 0303 health sciences, Ralstonia solanacearum, Ecology, biology, 030306 microbiology, Host (biology), fungi, Gene Transfer Techniques, Natural competence, Betaproteobacteria, food and beverages, Plants, Genetically Modified, biology.organism_classification, Genome, Plant, Bacteria, Food Science, Biotechnology
Abstract: The development of natural competence by bacteria in situ is considered one of the main factors limiting transformation-mediated gene exchanges in the environment. Ralstonia solanacearum is a plant pathogen that is also a naturally transformable bacterium that can develop the competence state during infection of its host. We have attempted to determine whether this bacterium could become the recipient of plant genes. We initially demonstrated that plant DNA was released close to the infecting bacteria. We constructed and tested various combinations of transgenic plants and recipient bacteria to show that the effectiveness of such transfers was directly related to the ratio of the complexity of the plant genome to the number of copies of the transgene.
Published: 2000

40. Quantification of bias related to the extraction of DNA directly from soils

Author: Pascal Simonet, Dominique Bernillon, Sylvie Clerc, Pascale Jeannin, Xavier Nesme, Francoise Le Gall, Åsa Frostegård, Vincent Ramisse, Sophie Courtois, 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), 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: DNA, Bacterial, Lysis, Microorganism, [SDV]Life Sciences [q-bio], Deoxyribonuclease HindIII, Applied Microbiology and Biotechnology, complex mixtures, 03 medical and health sciences, chemistry.chemical_compound, Bias, Actinomycetales, ComputingMilieux_MISCELLANEOUS, Soil Microbiology, 030304 developmental biology, 2. Zero hunger, Gel electrophoresis, Electrophoresis, Agar Gel, 0303 health sciences, Bacteriological Techniques, Ecology, biology, Bacteria, 030306 microbiology, Extraction (chemistry), Australia, General Microbial Ecology, biology.organism_classification, Bacteriophage lambda, chemistry, Biochemistry, DNA, Viral, Nucleic acid, Indicators and Reagents, France, Soil microbiology, DNA, Food Science, Biotechnology
Abstract: In recent years, several protocols based on the extraction of nucleic acids directly from the soil matrix after lysis treatment have been developed for the detection of microorganisms in soil. Extraction efficiency has often been evaluated based on the recovery of a specific gene sequence from an organism inoculated into the soil. The aim of the present investigation was to improve the extraction, purification, and quantification of DNA derived from as large a portion of the soil microbial community as possible, with special emphasis placed on obtaining DNA from gram-positive bacteria, which form structures that are difficult to disrupt. Furthermore, we wanted to identify and minimize the biases related to each step in the procedure. Six soils, covering a range of pHs, clay contents, and organic matter contents, were studied. Lysis was carried out by soil grinding, sonication, thermal shocks, and chemical treatments. DNA was extracted from the indigenous microflora as well as from inoculated bacterial cells, spores, and hyphae, and the quality and quantity of the DNA were determined by gel electrophoresis and dot blot hybridization. Lysis efficiency was also estimated by microscopy and viable cell counts. Grinding increased the extracellular DNA yield compared with the yield obtained without any lysis treatment, but none of the subsequent treatments clearly increased the DNA yield. Phage λ DNA was inoculated into the soils to mimic the fate of extracellular DNA. No more than 6% of this DNA could be recovered from the different soils. The clay content strongly influenced the recovery of DNA. The adsorption of DNA to clay particles decreased when the soil was pretreated with RNA in order to saturate the adsorption sites. We also investigated different purification techniques and optimized the PCR methods in order to develop a protocol based on hybridization of the PCR products and quantification by phosphorimaging.
Published: 1999

41. Ti plasmids from Agrobacterium characterize rootstock clones that initiated a spread of crown gall disease in Mediterranean countries

Author: Yves Dessaux, Delphine Héricher, Xavier Nesme, Sandrine Pionnat, Harald Keller, Andrée Bettachini, and Christine Poncet
Subjects: 0106 biological sciences, DNA, Bacterial, Agrobacterium, Biovar, Opine, Arginine, 01 natural sciences, Applied Microbiology and Biotechnology, DNA, Ribosomal, Polymerase Chain Reaction, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Ti plasmid, Plasmid, Plant Microbiology, Plant Tumors, RNA, Ribosomal, 16S, Botany, Gall, 0303 health sciences, Ecology, biology, Virulence, 030306 microbiology, Mediterranean Region, biology.organism_classification, chemistry, Nopaline, Restriction fragment length polymorphism, Polymorphism, Restriction Fragment Length, 010606 plant biology & botany, Food Science, Biotechnology, Plasmids, Rhizobium
Abstract: Crown gall caused by Agrobacterium is one of the predominant diseases encountered in rose cultures. However, our current knowledge of the bacterial strains that invade rose plants and the way in which they spread is limited. Here, we describe the integrated physiological and molecular analyses of 30 Agrobacterium isolates obtained from crown gall tumors and of several reference strains. Characterization was based on the determination of the biovar, analysis of 16S ribosomal DNA restriction fragment length polymorphisms by PCR (PCR-RFLP), elucidation of the opine type, and PCR-RFLP analysis of genes involved in virulence and oncogenesis. This study led to the classification of rose isolates into seven groups with common chromosome characteristics and seven groups with common Ti plasmid characteristics. Altogether, the rose isolates formed 14 independent groups, with no specific association of plasmid- and chromosome-encoded traits. The predominant Ti plasmid characteristic was that 16 of the isolates induced the production of the uncommon opine succinamopine, while the other 14 were nopaline-producing isolates. With the exception of one, all succinamopine Ti plasmids belonged to the same plasmid group. Conversely, the nopaline Ti plasmids belonged to five groups, one of these containing seven isolates. We showed that outbreaks of disease provoked by the succinamopine-producing isolates in different countries and nurseries concurred with a common origin of specific rootstock clones. Similarly, groups of nopaline-producing isolates were associated with particular rootstock clones. These results strongly suggest that the causal agent of crown gall disease in rose plants is transmitted via rootstock material.
Published: 1999

42. Direct conjugal transfers of Ti plasmid to soil microflora

Author: Xavier Nesme, S. Teyssier-Cuvelle, Christophe Mougel, ProdInra, Migration, 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, and Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)
Subjects: DNA, Bacterial, Agrobacterium, Sequence analysis, Auxotrophy, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Microbial Sensitivity Tests, Polymerase Chain Reaction, Microbiology, 03 medical and health sciences, Ti plasmid, RNA, Ribosomal, 16S, Genetics, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, DNA Primers, 0303 health sciences, biology, Base Sequence, 030306 microbiology, Drug Resistance, Microbial, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, Sinorhizobium, Conjugation, Genetic, Microbial genetics, Soil microbiology, Polymorphism, Restriction Fragment Length, Plasmids, Rhizobium
Abstract: The bacterial species in soil that can receive a Ti plasmid by conjugation from Agrobacterium spp. were investigated. In order to have direct access to the potential reservoir of Ti plasmid amongst soil microflora, the conjugal system consisting of a multiply auxotrophic derivative of C58 (ST-96-4) and a derivative of pTiC58Delta(acc)R (pSTiEGK) containing a triple antibiotic-resistance cassette in traM was used to transfer the Ti plasmid in a complex soil microflora used as the recipient. Numerous transconjugants were obtained by this method but none was identified as Agrobacterium. This could be explained by the low density of Agrobacterium in the tested soil. As indicated by analysis of the ribosomal gene rrs, transconjugants recovered directly from soil were found to be new bacterial species which appeared to be closely related to Sinorhizobium spp.
Published: 1999

43. During infection of its host, the plant pathogen Ralstonia solanacearum naturally develops a state of competence and exchanges genetic material

Author: Xavier Nesme, Belén Brito, Pascal Simonet, Franck Bertolla, Åsa Frostegård, 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), 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, Ralstonia solanacearum, biology, 030306 microbiology, Physiology, Host (biology), [SDV]Life Sciences [q-bio], fungi, Genetic transfer, food and beverages, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Marker gene, Microbiology, 03 medical and health sciences, Transformation (genetics), Botany, Agronomy and Crop Science, Gene, Pathogen, Bacteria, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: In this work we investigated the ability of the plant pathogen Ralstonia solanacearum to develop a state of competence in planta and to be genetically transformed during the infection process. Tomato plants infected with R. solanacearum GMI1000 were inoculated with plasmid DNA. R. solanacearum clones expressing the marker gene were selected only during the period of time that bacteria were actively multiplying inside the plant vessels. Moreover, experiments in which R. solanacearum strains harboring different marker genes were co-inoculated into the plant demonstrated that infecting bacterial strains exchange genetic information in planta by a mechanism that is likely to be transformation. To our knowledge, these results constitute the first demonstration of soil microorganisms developing a state of competence in planta. The biotechnological implications of this result will be discussed.
Published: 1999

44. Examen critique de l’analyse par RFLP du gène déterminant l’ARN 16S

Author: Louis Gardan, Charles Manceau, Xavier Nesme, Yves Dessaux, Annick Petit, Cécil Chomel, Phil M. Oger, Institut des Sciences Végétales, Centre National de la Recherche Scientifique (CNRS), Unité de recherche Pathologie végétale et phytobactériologie, Institut National de la Recherche Agronomique (INRA), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon
Subjects: 16S, lcsh:QH426-470, Bacterial population, Biology, RRS, PCR-RFLP, 03 medical and health sciences, AGROBACTERIUM, PSEUDOMONAS, XANTHOMONAS, Genetics, Genetics(clinical), Gene, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, lcsh:SF1-1100, 2. Zero hunger, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, 030306 microbiology, food and beverages, General Medicine, 16S ribosomal RNA, Full article, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Soil borne, Animal Science and Zoology, lcsh:Animal culture, Restriction fragment length polymorphism
Abstract: The value of the restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified rrs (16S ribosomal ribonucleic acid [rRNA] gene) for the rapid identification of bacteria isolated from soil or plants, and the limits of this technique, were evaluated using bacterial genera characteristic of the above-mentioned ecosystems. Results showed that up to two restriction site differences may occur between rrs operons within the same bacterial genome as well as between bacteria belonging to the same genospecies. In spite of these limited differences, members of the same genospecies yield very similar rrs RFLP patterns. The identification limit varies according to the analyzed taxa. Species can be differentiated amongst members of both the family Rhizobiaceae and the genus Stenotrophomonas, while the technique only allows grouping of closely related species amongst Xanthomonas spp. and amongst species related to Psendomonas syringae. On the basis of their rrs RFLP profiles, all presently known species of Agrobacterium can be routinely identified using only the enzymes HpaII (or MspI), AUIL and HaeIII. Moreover, the method was also found to be valuable in assessing the biodiversity of a bacterial community isolated from the rhizosphere. From the comparison of empiric rrs RFLPs, published sequences and deoxyribonucleic acid (DNA) pairing studies, we suggest that the occurrence of five different restriction sites within two rrs genes is the minimum difference required to clearly establish that two relevant bacteria belong to different genospecies., L’intérêt et les limites de l’identification bactérienne basée sur l’analyse du gène codant pour l’ARN ribosomique 16S par PCR-RFLP ont été évalués dans plusieurs genres bactériens typiques des écosystèmes sol et plante. Les résultats montrent qu’il peut y avoir jusqu’à deux sites de restriction différents entre les gènes rrs de bactéries appartenant à la même espèce génomique ou entre différents opérons d’un même génome. Les résultats permettent cependant d’identifier les bactéries jusqu’au niveau de l’espèce chez les Rhizobiaceae et chez Stenotrophomonas, et jusqu’au niveau du groupe d’espèces apparentées d’un même genre chez Xanthomonas et dans le groupe apparenté à P. syringae. De plus, la méthode s’est révélée parfaitement adaptée pour identifier et classer les bactéries isolées d’un peuplement rhizosphérique, en permettant une identification approchée du genre, voire de l’espèce. La comparaison des données de PCR-RFLP avec les données de séquences et d’hybridations ADN-ADN suggèrent qu’un minimum de cinq sites de restriction polymorphes dans le gène 16S est nécessaire pour affirmer que des bactéries appartiennent à des espèces génomiques différentes.
Published: 1998

45. Conditions for natural transformation of Ralstonia solanacearum

Author: Franck Bertolla, Xavier Nesme, Pascal Simonet, F Van Gijsegem, ProdInra, Migration, 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), Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-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, Bacterial, [SDV]Life Sciences [q-bio], Applied Microbiology and Biotechnology, Microbiology, Bacterial genetics, 03 medical and health sciences, chemistry.chemical_compound, Transformation, Genetic, Exponential growth, Sequence Homology, Nucleic Acid, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Ralstonia solanacearum, Ecology, biology, Models, Genetic, 030306 microbiology, food and beverages, biochemical phenomena, metabolism, and nutrition, BIOLOGIE MOLECULAIRE, biology.organism_classification, Molecular Weight, [SDV] Life Sciences [q-bio], Transformation (genetics), chemistry, Gram-Negative Aerobic Rods and Cocci, Homologous recombination, DNA, Bacteria, Recombination, Food Science, Biotechnology, Research Article
Abstract: The development of competence allowing natural transformation of Ralstonia solanacearum was found to occur during exponential growth and not in response to any excreted factors. Linear DNAs were effectively integrated by recombination requiring a minimum of 50 bp of homologous DNA. Therefore, DNA from other genera and species were ineffective.
Published: 1997

46. Detection and determination of pathogenic Agrobacterium of roses with PCR

Author: Xavier Nesme, S. Pionnat, Yves Dessaux, C. Poncet, Station de botanique et de pathologie végétale, Institut National de la Recherche Agronomique (INRA), Unité de recherche Pathologie végétale et phytobactériologie, and ProdInra, Migration
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Agrobacterium, [SDV]Life Sciences [q-bio], Horticulture, Biology, biology.organism_classification, 01 natural sciences, [SDV] Life Sciences [q-bio], 03 medical and health sciences, CRAWN GALL, POUVOIR PATHOGENE, Botany, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience
Published: 1996

47. Novel Tellurite-Amended Media and Specific Chromosomal and Ti Plasmid Probes for Direct Analysis of Soil Populations of Agrobacterium Biovars 1 and 2

Author: Christophe Mougel, Benoit Cournoyer, and Xavier Nesme
Subjects: 0303 health sciences, 03 medical and health sciences, Ecology, 030306 microbiology, Applied Microbiology and Biotechnology, Food Science, Biotechnology
Published: 2001

48. Connaissance et gestion des ressources génétiques = Current knowledge and management of genetic resources

Author: Charles Manceau, Sylvie Baucheron, Patrick Robbe, Jean Thioulouse, Jerome Etienne, Elisabeth Chaslus-Dancla, Françoise Forey, Jérôme Briolay, Mare Neyra, Xavier Nesme, Karine Groud, Renaud Nalin, Sylvie Teyssier, Sophie Jarraud, Cathy d’Angelo, François Vandenesch, Karim Sidi-Boumedine, Axel Cloeckaert, Hélène Meugnier, Michele Péloille, Christophe Mougel, Gerard Lina, 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), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [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)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: IV — Inventaire, Caractérisation et Suivi de la Diversité Microbienne / Inventory, Characterization and Monitoring of Microbial Diversity, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Population, ADN, Computational biology, BACTERIE, espèce génomique, TECHNIQUE AFLP, Genome, aflp, Restriction fragment, distance génétique, 03 medical and health sciences, Intergenic region, Genetics, TECHNIQUE PCR, ETUDE COMPARATIVE, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Phage typing, ANALYSE NUMERIQUE, 2. Zero hunger, 0303 health sciences, education.field_of_study, Genetic diversity, DISTANCE GENETIQUE, biology, IDENTIFICATION, 030306 microbiology, food and beverages, General Medicine, Ribosomal RNA, DIVERSITE GENETIQUE, population bactérienne, diversité intraspécifique, biology.protein, ETUDE EXPERIMENTALE, Animal Science and Zoology, Amplified fragment length polymorphism, ANALYSE GENETIQUE
Abstract: The reliability and the level of taxonomie resolution of the amplified fragment length polymorphism (AFLP) method were evaluated with species of patho-genic bacteria involved in human, animal and plant diseases. The method was found to be very versatile as it can be adapted to the individual genome constraints of all tested species. The calculation of a genetic distance d corresponding to the average dissimilarity between actual overall genome sequences was proposed for comparing AFLP data. Bacterial models showed clearly different patterns between strains be-longing to different genomic species, while patterns were clearly similar within a given species. The threshold which distinguishes between inter and infra-specific distances indicates a critical overall genome diversity of about 14% (d = 0.14). AFLP had more resolution power than serology, phage typing, PFGE and restriction analysis of ribosomal intergenic spacers. In the latter case, regression analysis showed that PCR-RFLP of ribosomal intergenic spacers can only be used to differentiate bacteria which have at least 3.4% (d — 0.034) nucleotide differences between their respec-tive genomes. Finally, an improved procedure using newly developed software was also proposed in order to standardize the capture of reliable data and their numeric treatment for the future development of AFLP data bases.; La reproductibilité et Ie niveau de resolution taxo-nomique de ramplification aléatoire de fragments de restriction (AFLP) ont été éval-ués avec divers modèles pathogènes de l’homme, des animaux et des plantes. La methode est tres adaptable et peut être modifiée en fonction des particularités génomiques de chaque espèce. La différence nucléotidique moyenne réelle entre les genomes est une mesure de la distance génomique entre bactéries qui peut être estimée a partir de l’AFLP. Cette mesure permet la comparaison de données AFLP obtenues de fagons différentes. Avec la plupart des modèles, Ie seuil discriminant les distances interdes distances infra-spécifiques correspond a des differences nucléotidiques de l’ordre de 14% (d — 0,14). L’AFLP s’est montrée plus résolutive que la sérologie, la lyso-typie, l’électrophorèse en champs pulsés, et la PCR-RFLP de l’intergène ribosomique. L’analyse montre ainsi que la PCR-RFLP de l’intergène ribosomique permet de dis-tinguer des bactéries présentant au moins 3,4% (d = 0,034) de differences entre leurs genomes respectifs. Une procédure Standard d’aquisition et de traitement numérique des données incluant des logiciels adaptés est également proposée.

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