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

Author: Marie Larousse, Corinne Rancurel, Camille Syska, Ferran Palero, Catherine Etienne, Benoît Industri, Xavier Nesme, Marc Bardin, and Eric Galiana
Subjects: Oomycete, Biofilm, Host plant, Metagenomics 16S, Flavobacteriaceae, Pseudomonadaceae, Microbial ecology, QR100-130
Abstract: Abstract 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.
Published: 2017
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3. Diversifying Anaerobic Respiration Strategies to Compete in the Rhizosphere

Author: Solène M. Lecomte, Wafa Achouak, Danis Abrouk, Thierry Heulin, Xavier Nesme, and Feth el Zahar Haichar
Subjects: rhizosphere competence, anaerobic respiration, terminal electron acceptors, respiratory pathways, rhizobacteria, root colonization, Environmental sciences, GE1-350
Abstract: The rhizosphere is the interface between plant roots and soil where intense, varied interactions between plants and microbes influence plants' health and growth through their influence on biochemical cycles, such as the carbon, nitrogen, and iron cycles. The rhizosphere is also a changing environment where oxygen can be rapidly limited and anaerobic zones can be established. Microorganisms successfully colonize the rhizosphere when they possess specific traits referred to as rhizosphere competence. Anaerobic respiration flexibility contributes to the rhizosphere competence of microbes. Indeed, a wide range of compounds that are available in the rhizosphere can serve as alternative terminal electron acceptors during anaerobic respiration such as nitrates, iron, carbon compounds, sulfur, metalloids, and radionuclides. In the presence of multiple terminal electron acceptors in a complex environment such as the rhizosphere and in the absence of O2, microorganisms will first use the most energetic option to sustain growth. Anaerobic respiration has been deeply studied, and the genes involved in anaerobic respiration have been identified. However, aqueous environment and paddy soils are the most studied environments for anaerobic respiration, even if we provide evidence in this review that anaerobic respiration also occurs in the plant rhizosphere. Indeed, we provide evidence by performing a BLAST analysis on metatranscriptomic data that genes involved in iron, sulfur, arsenate and selenate anaerobic respiration are expressed in the rhizosphere, underscoring that the rhizosphere environment is suitable for the establishment of anaerobic respiration. We thus focus this review on current research concerning the different types of anaerobic respiration that occur in the rhizosphere. We also discuss the flexibility of anaerobic respiration as a fundamental trait for the microbial colonization of roots, environmental and ecological adaptation, persistence and bioremediation in the rhizosphere. Anaerobic respiration appears to be a key process for the functioning of an ecosystem and interactions between plants and microbes.
Published: 2018
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4. Ralstonia solanacearum Virulence Increased Following Large Interstrain Gene Transfers by Natural Transformation

Author: Bénédicte Coupat-Goutaland, Dominique Bernillon, Alice Guidot, Philippe Prior, Xavier Nesme, and Franck Bertolla
Subjects: Microbiology, QR1-502, Botany, QK1-989
Abstract: 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 significant increase 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
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5. GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands.

Author: Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, Laurent Duret, and Vincent Daubin
Subjects: Genetics, QH426-470
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.
Published: 2015
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6. During Infection of Its Host, the Plant Pathogen Ralstonia solanacearum Naturally Develops a State of Competence and Exchanges Genetic Material

Author: Franck Bertolla, Åsa Frostegård, Belen Brito, Xavier Nesme, and Pascal Simonet
Subjects: genetic transfer, Microbiology, QR1-502, Botany, QK1-989
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
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7. 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

8. 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

9. 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

10. Évaluation du risque simplifiée du tomato brown rugose fruit virus pour la France métropolitaine

Author: Eric Verdin, Pascal Gentit, Stéphan Steyer, Thierry Wetzel, Thomas Le Bourgeois, Marie-Helene Balesdent, Françoise Binet, Antonio Biondi, Philippe Castagnone, Péninna Deberdt, Nicolas Desneux, Marie Laure Desprez Loustau, Abraham ESCOBAR GUTIERREZ, Laurent Gentzbittel, Herve Jactel, David Makowski, Arnaud Monty, Maria Navajas, Xavier Nesme, Marie-Hélène Robin, François Verheggen, Christine Tayeh, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre Wallon de Recherches Agronomiques (CRA-W), Dienstleistungszentren Ländlicher Raum Rheinland-Pfalz, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université de Catane, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Centre International de Recherche sur l'Environnement et le Développement (CIRED), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École des hautes études en sciences sociales (EHESS)-AgroParisTech-École des Ponts ParisTech (ENPC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Liège, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire 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), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Unité Entomologie fonctionnelle et évolutive, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail, Contrat : 2019-SA-0080, Commanditaire : Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (France), Type de commande : Commande avec contrat/convention/lettre de saisine, Date de signature : 2019-04-25, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (Cirad-Persyst-UPR 103 HORTSYS), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biodiversité, Gènes et Communautés, Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École des hautes études en sciences sociales (EHESS)-AgroParisTech, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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: risque phytosanitaire, virus phytopathogène, analyse de risques, description de symptomes, dissémination, tomato brown rugose fruit virus, état de l'art, semences, maladie émergente, culture legumiere, expertise scientifique, évaluation du risque, tobamovirus, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, piment, filière économique, tomate, phytopathogenic virus, outbreaks, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, emerging disease, résistance, pathologie végétale, épidémie
Abstract: Évaluation du risque simplifiée du tomato brown rugose fruit virus pour la France métropolitaine. Avis de l'Anses. Rapport d'expertise collective
Published: 2020

11. 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

12. 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

13. Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions

Author: Nesrine Nabi, Ahmed Ben Hafsa, Vincent Gaillard, Xavier Nesme, Maher Chaouachi, and Ludovic Vial
Subjects: DNA, Bacterial, Virulence, Neoplasms, Plant Tumors, Genetics, Humans, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Plasmids, Rhizobium
Abstract: Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating "classic" Ti plasmids (with one or two T-DNAs) and "Ri and vine-Ti" plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.
Published: 2018

14. 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

15. Risque phytosanitaire (ARP) portant sur Fusarium oxysporum f. sp. cubense (agent pathogène responsable de la maladie de Panama) pour les départements d'Outre-mer

Author: Marie-Helene Balesdent, Yolande Chilin Charles, David Makowski, Christian Steinberg, Pierre Silvie, Philippe Castagnone, Bruno Chauvel, Nicolas Desneux, Marie Laure Desprez Loustau, Abraham ESCOBAR GUTIERREZ, Laurent Gentzbittel, Herve Jactel, Thomas Le Bourgeois, Xavier Nesme, Stéphan Steyer, Frederic Suffert, Eric Verdin, François Verheggen, Thierry Wetzel, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agronomie, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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 Wallon de Recherches Agronomiques (CRA-W), Station de Pathologie Végétale (AVI-PATHO), Unité Entomologie fonctionnelle et évolutive, Université de Liège, DLR Rheinpfalz, Institute of Plant Protection, and Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail
Subjects: Analyse de risque phytosanitaire, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, outre mer français, état de l'art, risque économique, race tropicale 4, regulation, weed control methods, champignon phytopathogène, expertise scientifique, banane, phytopathogenic fungus, détection, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Foc TR4, méthode de lutte, maladie de Panama, Fusarium oxysporum f. sp. cubense, réglementation, pathologie végétale, économie des filières
Abstract: Risque phytosanitaire (ARP) portant sur [i]Fusarium oxysporum[/i] f. sp.[u] cubense[/u] (agent pathogène responsable de la maladie de Panama) pour les départements d'Outre-mer
Published: 2018

16. Connaissances nécessaires à la gestion du risque 'écorces sensibles au nématode du pin'

Author: Philippe Castagnone, Herve Jactel, Philippe Reignault, Marie-Helene Balesdent, Bruno Chauvel, Nicolas Desneux, Marie Laure Desprez Loustau, Abraham ESCOBAR GUTIERREZ, Laurent Gentzbittel, Thomas Le Bourgeois, Xavier Nesme, Pierre Silvie, Stéphan Steyer, Eric Verdin, François Verheggen, Thierry Wetzel, 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), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Université du Littoral Côte d'Opale (ULCO), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre Wallon de Recherches Agronomiques (CRA-W), Station de Pathologie Végétale (AVI-PATHO), Unité Entomologie fonctionnelle et évolutive, Université de Liège, DLR Rheinpfalz, Institute of Plant Protection, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université du Littoral Côte d’Opale (ULCO), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, lutte contre les nématodes, état de l'art, transmission, forestry tractors, copeau, expertise scientifique, insect vectors, méthode de transmission, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Bursaphelenchus xylophilus, nematode control, vecteur de maladies, disease vector, nématode du pin, Monochamus galloprovincialis, insecte vecteur, matériel forestier, pathologie végétale, écorce
Abstract: Connaissances nécessaires à la gestion du risque "écorces sensibles au nématode du pin"
Published: 2018

17. Analyse de risque phytosanitaire portant sur la berce du Caucase

Author: Arnaud Albert, Guillaume Fried, Thomas Le Bourgeois, Marie-Helene Balesdent, Françoise Binet, Antonio Biondi, Philippe Castagnone, Christophe Clement, Péninna Deberdt, Nicolas Desneux, Marie Laure Desprez Loustau, Abraham ESCOBAR GUTIERREZ, Laurent Gentzbittel, Herve Jactel, David Makowski, Arnaud Monty, Maria Navajas Navarro, Xavier Nesme, Stéphan Steyer, Eric Verdin, François Verheggen, Thierry Wetzel, Ecologie des espèces envahisantes, Agence Française de la Biodiversité, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université de Catane, 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), Université de Reims Champagne-Ardenne (URCA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Agronomie, Université de Liège, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Wallon de Recherches Agronomiques (CRA-W), Station de Pathologie Végétale (AVI-PATHO), Unité Entomologie fonctionnelle et évolutive, DLR Rheinpfalz, Institute of Plant Protection, and Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail
Subjects: éradication de la maladie, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, état de l'art, weed control methods, santé humaine, expertise scientifique, human health, berce du Caucase, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, méthode de lutte, union européenne, espèce exotique invasive, analyse de risque phytosanitaire, réseau de surveillance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Heracleum mantegazzianum
Abstract: Analyse de risque phytosanitaire portant sur la berce du Caucase
Published: 2018

18. Risques et bénéfices relatifs des alternatives aux produits phytopharmaceutiques comportant des néonicotinoïdes: Tome 1 – Rapport du groupe de travail Identification des alternatives aux usages autorisés des néonicotinoïdes

Author: Herve Jactel, Romain Bonafos, Robert Delorme, Eric Thybaud, Denis Thiery, Philippe Reignault, Marie-Helene Balesdent, Philippe Castagnone, Bruno Chauvel, Nicolas Desneux, Marie Laure Desprez Loustau, Abraham ESCOBAR GUTIERREZ, Laurent Gentzbittel, Thomas Le Bourgeois, Xavier Nesme, Pierre Silvie, Stéphan Steyer, Frederic Suffert, Valérie Verdier, Eric Verdin, François Verheggen, Thierry Wetzel, Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Chercheur indépendant, Institut National de l'Environnement Industriel et des Risques (INERIS), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Université du Littoral Côte d'Opale (ULCO), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre Wallon de Recherches Agronomiques (CRA-W), UMR Résistance des plantes aux bioagresseurs, Institut de Recherche pour le Développement (IRD [Bolivie]), Station de Pathologie Végétale (AVI-PATHO), Unité Entomologie fonctionnelle et évolutive, Université de Liège, DLR Rheinpfalz, Institute of Plant Protection, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université du Littoral Côte d’Opale (ULCO), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, insecte pollinisateur, indicateurs de risque, néonicotinoïdes, état de l'art, public health, insecticide, expertise scientifique, environmental impact, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, santé publique, méthodes de lutte alternatives, organismes nuisibles, impact environnemental, organisme nuisible, lutte alternative, pests, évaluation économique
Abstract: Risques et bénéfices relatifs des alternatives aux produits phytopharmaceutiques comportant des néonicotinoïdes. Tome 1 – Rapport du groupe de travail Identification des alternatives aux usages autorisés des néonicotinoïdes
Published: 2018

19. 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

20. 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

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

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

22. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis

Author: Xavier Nesme, Florent Lassalle, Daniel Muller, 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) [ANR-BLAN-08-0090], AGROMICS (ENVIROMICS challenge of the Interdisciplinary Mission of the CNRS), European Project: 260801,EC:FP7:ERC,ERC-2010-StG_20091118,BIG_IDEA(2010), 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: Genetic Speciation, [SDV]Life Sciences [q-bio], Niche, ecotype, core niche, Bacterial genome size, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Ecological speciation, Species Specificity, ecological speciation, ecological niche, Reverse ecology, Molecular Biology, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS, Ecological niche, Experimental evolution, Bacteria, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], bacterial speciation, General Medicine, Genomics, Adaptation, Physiological, Biological Evolution, Cladogenesis, core genome, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial
Abstract: International audience; In this review, we synthesise current models and recent comparative genomic studies describing how bacterial species may emerge through adaptation to a new ecological niche and maintain themselves in the same niche over long time periods. We notably consider the impact of genetic exchange with phylogenetically close relatives living in sympatry and how this leads to the heterogeneous evolution of different genes within the bacterial genome. This heterogeneity provides landmarks to recognise genes that determine adaptation to the ecological niche, and we present reverse ecology strategies to unravel ecological properties of bacterial populations. Crown Copyright (C) 2015 Published by Elsevier Masson SAS on behalf of Institut Pasteur.
Published: 2015

23. 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

24. Revised phylogeny of [i]Rhizobiaceae[/i]: Proposal of the delineation of [i]Pararhizobium gen. nov.[/i], and 13 new species combinations

Author: Xavier Nesme, Philippe de Lajudie, Kristina Lindström, Seyed Abdollah Mousavi, Anne Willems, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Department of Environmental Sciences, Faculty of Science, Department of Biochemistry and Microbiology, Laboratory of Microbiology, Ghent University [Belgium] ( UGENT ), 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 des symbioses tropicales et méditerranéennes ( LSTM ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université Montpellier 1 ( UM1 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Academy of Finland [132544], Societas Scientiarum Fennica, Oskar Oflund Foundation, Universiteit Gent = Ghent University [Belgium] (UGENT), 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 des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ghent University [Belgium] (UGENT), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: DNA, Bacterial, MLSA, food.ingredient, Rhizobiaceae, Agrobacterium, Molecular Sequence Data, housekeeping genes, Applied Microbiology and Biotechnology, Microbiology, food, Genus, Pararhizobium, Botany, Ecology, Evolution, Behavior and Systematics, Phylogeny, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Housekeeping genes, Genes, Essential, Ciceribacter, biology, Phylogenetic tree, rhizobiaceae, biology.organism_classification, Genes, Bacterial, Sinorhizobium, Neorhizobium, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Multilocus Sequence Typing
Abstract: The family Rhizobiaceae accommodates the seven genera Rhizobium, Neorhizobium, Allorhizobium, Agrobacterium, Ensifer (syn. Sinorhizobium), Shinella and Ciceribacter. However, several so-called Rhizobium species do not exhibit robust phylogenetic positions. Rhizobium is extremely heterogeneous and is in need of major revision. Therefore, a phylogenetic examination of the family Rhizobiaceae by multilocus sequence analysis (MLSA) of four housekeeping genes among 100 strains of the family was undertaken. Based on the results we propose the delineation of the new genus Pararhizobium in the Rhizobiaceae family, and 13 new species combinations: Agrobacterium nepotum comb. nov., Agrobacterium pusense comb. nov., Agrobacterium skierniewicense comb. nov., Allorhizobium vitis comb. nov., Allorhizobium taibaishanense comb. nov., Allorhizobium paknamense comb. nov., Allorhizobium oryzae comb. nov., Allorhizobium pseudoryzae comb. nov., Allorhizobium borbori comb. nov., Pararhizobium giardinii comb. nov., Pararhizobium capsulatum comb. nov., Pararhizobium herbae comb. nov., and Pararhizobium sphaerophysae comb. nov.
Published: 2015

25. 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

26. 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

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

Author: Ramon Rossello-Mora, Martin Maiden, Erko Stackebrandt, Xavier Nesme, Peter Kampfer, Patrick Grimont, Alan Ward, William Whitman, and George Garrity
Subjects: General Medicine, Microbiology, Ecology, Evolution, Behavior and Systematics
Published: 2002

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

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

29. 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

30. 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

31. IMPACT OF THE CROWN GALL DISEASE ON VIGOUR AND YIELD OF ROSE TREES

Author: D. Hericher, C. Poncet, S. Pionnat, Xavier Nesme, L. Simonini, Yves Dessaux, A. Bettachini, and C. Antonini
Subjects: Rose (mathematics), Horticulture, Yield (wine), Crown (botany), Gall, Biology
Published: 1996

32. 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

33. Diversity and Genetic Relatedness within Genera Xanthomonas and Stenotrophomonas Using Restriction Endonuclease Site Differences of PCR-amplified 16S rRNA Gene

Author: Xavier Nesme, Mario Vaneechoutte, Jean Swings, Bart Hoste, and Stephanie Orso
Subjects: Genetics, biology, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, Applied Microbiology and Biotechnology, Microbiology, Restriction enzyme, Restriction map, Xanthomonas, Stenotrophomonas, Restriction fragment length polymorphism, Xylella fastidiosa, Ecology, Evolution, Behavior and Systematics
Abstract: Summary Restriction maps of PCR-amplified 16s rRNA genes ( rrs for ribosomal rRNA small subunit) were prepared and compared for 43 Xanthomonas and Stenotrophomonas strains belonging to representative DNA-DNA similarity groups. Nineteen restriction fragment length polymorphisms (RFLPs) were distinguished, forming two main clusters: one contained all Xanthomonas species, the other contained strains of Stenotrophomonas spp. (formerly named X. maltophilia ). The genera Xanthomonas and Stenotrophomonas appeared to form a coherent group excluding Xylella fastidiosa . The rrs RFLP permitted to differentiate X. fragariae, X. oryzae, X. axonopodis, X. populi pv. populi from most pathovars of X. campestris . The latter species had very closely related patterns, contrary to X. albilineans, X. campestris pv. hyacinthi and pv. graminis , and a X. campestris strain (isolated from Saccharum officinarum , Guadeloupe) whic formed a more distinct subcluster. All genospecies of Stenotrophomonas had different rrs patterns, and appeared to form a less coherent taxon. Relationships between the percentage of DNA-DNA hybridization and the rate of nucleotide substitution in rrs confirmed the clear delineation of the two genera.
Published: 1995

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. Chromosomal and pTi genotypes of agrobacterium strains isolated from Populus tumors in two nurseries

Author: Philippe Normand, Xavier Nesme, C. Ponsonnet, and C. Picard
Subjects: Genetics, Rhizobiaceae, Ecology, Agrobacterium, Plant Tumors, Agrobacterium tumefaciens, Biology, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Ti plasmid, Plasmid, Botany, Genotype, Gall
Abstract: Agrobacterium tumefaciens strains isolated from aspen tumors have been characterized in order to study Ti plasmid stability in different chromosomal backgrounds under natural conditions. Chromosomal and pTi genotypes were characterized by DNA-DNA hybridization. Single tumors contained one to four strains of A. tumefaciens as characterized by their chromosomal genotypes and one or two different nopaline-type pTi genotypes. Genotypes of pTi were associated with identical chromosomal backgrounds in different tree nurseries, suggesting that pTi plasmids are stably maintained in the small set of strains causing the present aspen crown gall outbreaks.
Published: 1992

43. 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

44. 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

45. 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

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

Author: Bénédicte, Coupat, Fanny, Chaumeille-Dole, Saliou, Fall, Philippe, Prior, Pascal, Simonet, Xavier, Nesme, and Franck, Bertolla
Subjects: DNA, Bacterial, Gene Transfer, Horizontal, Genes, Bacterial, Ralstonia solanacearum, Transformation, Bacterial, Genome, Bacterial, Phylogeny, Plasmids
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

47. Section 2 update: Detection of microbial nucleic acid sequences

Author: Xavier Nesme, Christine Picard, and Pascal Simonet
Subjects: Section (archaeology), Chemistry, Nucleic acid, Combinatorial chemistry
Published: 2008

48. 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

49. 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

50. 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

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