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8. How to name those to blame: A practical taxonomical study of the Xanthomonas causing bacterial leaf spot of lettuce has major consequences for the boundaries delimitation of X. hortorum

Author

Morinière, Lucas, Burlet, Alexandre, Rosenthal, Emma, Nesme, Xavier, Portier, Perrine, Bull, Carolee, Lavire, Céline, Fischer-Le Saux, Marion, Bertolla, Franck, 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)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and 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)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

International audience; Assessment of the taxonomy and diversity of the Xanthomonas strains causing bacterial leaf spot of lettuce (BLSL), commonly referred to as X. campestris pv. vitians, has been a long-lasting issue which held back the global efforts made to understand this pathogen. In order to provide a sound basis essential to its study, we conducted a polyphasic approach on a panel of strains obtained through sampling campaigns or acquired from collections. Results of a multilocus sequence analysis combined with phenotypic assays revealed that the pathotype strain of X. campestris pv. vitians does not match the description of the nomenspecies provided by Brown in 1918 [1]. However, LMG 938 = CFBP 8686 does fit this description. Therefore, we propose that LMG 938 = CFBP 8686 replaces LMG 937 = CFBP 2538 as pathotype strain of X. campestris pv. vitians. Then, overall genome relatedness indices (OGRIs) calculations and crossed-pathogenicity assays on lettuce allowed to validate the nomenclature X. hortorum pv. vitians comb. nov. originally proposed by Vauterin et al. in 1995 [2]. Interestingly, genome-based phylogenies exhibited an evolutionary continuum between closely related species X. hortorum and X. cynarae, confirmed by multiple OGRIs calculations between all the taxonomically relevant members of these two species. Phenotypic profiles characterized with Biolog GEN III microplates did not reveal any stable diagnostic traits legitimizing the distinction into two different species but a strong stable core phenotype. Thus, to be in accordance with nowadays standards in bacterial taxonomy and with respect to the global taxonomical framework of the genus Xanthomonas [3, 4], we propose the new combination of X. hortorum Vauterin et al. 1995 and X. cynarae (Trébaol 2000) Timilsina et al. 2018 into a new X. hortorum comb. nov. This new stable species would allow to integrate new uncharacterized members of X. hortorum isolated over the years on a wide range of host plants, making it a promising model for the study of genomic and ecologic determinants underlying adaptation to host plants. 1. Brown NA. Some bacterial diseases of lettuce. J Agric Res 1918;13:367. 2. Vauterin L, Hoste B, Kersters K, Swings J. Reclassification of Xanthomonas. Int J Syst Evol Microbiol 1995;45:472-489. 3. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461-466. 4. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38:209-216.

Published
2020

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

Author

Sanguin, Herve, Remenant. Benoit, Dechesne, Arnaud, Thioulouse, Jean, Vogel, Timothy L., Nesme, Xavier, Moenne-Loccoz, Yvan, and Grundmann, Genevieve L.

Subjects
Agrobacterium tumefaciens -- Genetic aspects, Ribosomal RNA -- Research, Ribosomal RNA -- Structure, Rhizosphere -- Research, Soil biology -- Research, Biological sciences
Abstract

Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important and the high-throughput analysis of potential of taxonomic microarray should match the breadth of bacterial diversity. 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.

Published
2006

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

Author

Singh, Nitin K., Lavire, Céline, Nesme, Joseph, Vial, Ludovic, Nesme, Xavier, Mason, Christopher E., Lassalle, Florent, and Venkateswaran, Kasthuri

Subjects
COMPARATIVE genomics, SPACE stations, AGROBACTERIUM, MOBILE genetic elements, AGROBACTERIUM tumefaciens, GENOMICS
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, gyr B 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. [ABSTRACT FROM AUTHOR]

Published
2021
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15. Who’s who : Resolving the taxonomy of the causal agent of bacterial leaf spot of lettuce through a polyphasic approach leads to combine Xanthomonas hortorum Vauterin et al. 1995 and Xanthomonas cynarae (Trébaol 2000) Timilsina et al. 2018

Author

Morinière, Lucas, Burlet, Alexandre, Rosenthal, Emma, Nesme, Xavier, Portier, Perrine, Bull, Carolee, Lavire, Céline, Fischer-Le Saux, Marion, Bertolla, Franck, 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), 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), AGROCAMPUS OUEST, and 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 la Recherche Agronomique (INRA)-Université d'Angers (UA)

Subjects
taxonomy, [SDV]Life Sciences [q-bio], Xanthomonas hortorum, Xanthomonas cynarae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, bacterial leaf spot of lettuce, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

International audience; Assessment of the taxonomy and diversity of the Xanthomonas strains causing bacterial leaf spot of lettuce (BLSL), commonly referred as Xanthomonas campestris pathovar vitians, has been a long-lasting issue which held back the global efforts made to understand this disease and struggle against the damages it causes in the field. In order to restore sane bases essential to the study of this pathogen, we conducted an extensive polyphasic approach on a panel of strains obtained through sampling campaigns or collection strains acquisitions. Results of a multilocus sequence analysis crossed with pathogenicity assays revealed that BLSL-causing strains formed a monophyletic pathovar sparsely diversified in three clonal groups. However, genome-based phylogenies yielded only two major groups of strains. From the bigger picture perspective, phylogenies exhibited the intermediate position of pathovar vitians between close species X. hortorum and X. cynarae, resulting in a phylogenetic continuum regarding the known diversity of the genus. Finally, whole-genome comparisons of all type, pathotype or representative strains of these two species by multiple overall genome relatedness indices (OGRIs) calculation endorsed the hypothesis of one single specie. Carbon and nitrogen sources utilization tested using Biolog microplates did not revealed any particular phenotypic differences which would have legitimate the distinction into two species. Therefore, we propose the combination of X. hortorum, X. cynarae and X. campestris pv. vitians into a new X. hortorum comb. nov. with CFBP 4925 T = LMG 937 T remaining the type strain, and LMG 938 neoPT = NCPB 2248 neoPT becoming the pathotype strain of X. hortorum pv. vitians.

Published
2019

20. Diversifying anaerobic respiration strategies to compete in the rhizosphere

Author

Lecomte, Solène, Achouak, Wafa, ABROUK, Danis, Heulin, Thierry, Nesme, Xavier, Haichar, Feth El Zahar, 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), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), ANR [ANR-18-CE32-0005], ANR-18-CE32-0005,DIORE,Régulation de la dénitrification par la nature des exsudats racinaires(2018), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-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), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and ANR-18-CE32-0005,DIORE,Régulation de la dénitrification par la nature des exsudats racinaires

Subjects
lcsh:GE1-350, rhizosphere competence, fungi, adaptation, respiration anaérobie, anaerobic respiration, terminal electron acceptors, colonisation racinaire, rhizobacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, root colonization, rhizosphère, rhizobactérie, lcsh:Environmental sciences, respiratory pathways
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 O-2, 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

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

Author

Moriniere, Lucas, Burlet, Alexandre, Portier, Perrine, Lavire, Céline, Nesme, Xavier, Bertolla, Franck, 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), Station d’Expérimentation Rhône-Alpes Information Légumes, SERAIL, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and 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)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

International audience

Published
2018
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22. Diversifying anaerobic respiration strategies to compete in the rhizosphere

Author

Lecomte, Solène M., Achouak, Wafa, Abrouk, Danis, Heulin, Thierry, Nesme, Xavier, and Haichar, Feth-El-Zahar

Subjects
Biodiversity and Ecology, Biodiversité et Ecologie, rhizosphere competence, anaerobic respiration, terminal electron acceptors, respiratory pathways, rhizobacteria, root colonization, adaptation, fungi, colonisation racinaire, respiration anaérobie, rhizosphère, rhizobactérie
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 O-2, 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

23. Experimental and theoretical evaluation of typing methods based upon random amplification of genomic restriction fragments (AFLP) for bacterial population genetics

Author

Mougel, Christophe, Teyssier, Sylvie, d’Angelo, Cathy, Groud, Karine, Neyra, Mare, Sidi-Boumedine, Karim, Cloeckaert, Axel, Peloille, Michèle, Baucheron, Sylvie, Chaslus-Dancla, Élisabeth, Jarraud, Sophie, Meugnier, Hélène, Forey, Françoise, Vandenesch, François, Lina, Gérard, Étienne, Jéröme, Thioulouse, Jean, Manceau, Charles, Robbe, Patrick, Nalin, Renaud, Briolay, Jéröme, and Nesme, Xavier

Published
2001
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24. Agrobacterium fabrum C58 involved nitrate reductase NapA and antisense RNA NorR to denitrify.

Author

Lecomte, Solène, Nesme, Xavier, Franzino, Théophile, Villard, Camille, Pivard, Mariane, Vial, Ludovic, Doré, Jeanne, Hommais, Florence, and Haichar, Feth el Zahar

Subjects
*ANTISENSE RNA, *NITRATE reductase, *AGROBACTERIUM, *NON-coding RNA, *DENITRIFICATION, *PLANT roots
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. [ABSTRACT FROM AUTHOR]

Published
2021
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26. Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers

Author

Portier, Perrine, Saux, Marion Fischer-Le, Mougel, Christophe, Lerondelle, Catherine, Nesme, Xavier, Chapulliot, David, and Thioulouse, Jean

Subjects
Bacterial genetics -- Research, Agrobacterium tumefaciens -- Environmental aspects, Agrobacterium tumefaciens -- Genetic aspects, Agrobacterium tumefaciens -- Identification and classification, Biological sciences
Abstract

A study aims to facilitate high-throughput identification of agrobacteria using the AFLP methodology, which is useful for genomic species identification and infraspecific typing of a large number of strains. Catalogues of specific AFLP genomic markers, which are conserved among all genomic species members, are established using a set of 52 agrobacterial strains from international collections, and there is a particular emphasis on the three most frequent genomic species of Agrobacterium biovar 1, genomic species G1, G4, and G8.

Published
2006

27. Small RNA deep-sequencing analyses reveal a new regulator of virulence in Agrobacterium fabrum C58

Author

Dequivre, Magali, Diel, Benjamin, Villard, Camille, Sismeiro, Odile, Durot, Maxime, Coppée, Jean-Yves, Nesme, Xavier, VIAL, Ludovic, Hommais, Florence, 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), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), This study was supported by the EcoGenome project of the French Agence Nationale de la Recherche [grant number ANR-BLAN-08-0090], PEPS INSB and PEPII INSB-INEE-INSMI-INS2I ' Bio-Math-Info' funding from the Centre National de la Recherche Scientifique. M. Dequivre received a doctoral grant from the French Ministère de l’Education nationale de l’Enseignement Supérieur et de la Recherche, 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], 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), 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), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), 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 ), 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 ), Transcriptome et Epigénome ( PF2 ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), 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, Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), 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), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Base Sequence, Virulence, Sequence Analysis, RNA, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Agrobacterium, High-Throughput Nucleotide Sequencing, Gene Expression Regulation, Bacterial, Sequence Analysis, DNA, RNA, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], RNA, Small Untranslated, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RNA, Messenger, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Transcriptome, ComputingMilieux_MISCELLANEOUS, Gene Library, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Novel ways of regulating Ti plasmid functions were investigated by studying small RNAs (sRNAs) that are known to act as posttranscriptional regulators in plant pathogenic bacteria. sRNA-seq analyses of Agrobacterium fabrum C58 allowed us to identify 1,108 small transcripts expressed in several growth conditions that could be sRNAs. A quarter of them were confirmed by bioinformatics or by biological experiments. Antisense RNAs represent 24% of the candidates and they are over-represented on the pTi (with 62% of pTi sRNAs), suggesting differences in the regulatory mechanisms between the essential and accessory replicons. Moreover, a large number of these pTi antisense RNAs are transcribed opposite to those genes involved in virulence. Others are 5′- and 3′-untranslated region RNAs and trans-encoded RNAs. We have validated, by rapid amplification of cDNA ends polymerase chain reaction, the transcription of 14 trans-encoded RNAs, among which RNA1111 is expressed from the pTiC58. Its deletion decreased the aggressiveness of A. fabrum C58 on tomatoes, tobaccos, and kalanchoe, suggesting that this sRNA activates virulence. The identification of its putative target mRNAs (6b gene, virC2, virD3, and traA) suggests that this sRNA may coordinate two of the major pTi functions, the infection of plants and its dissemination among bacteria.

Published
2015

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

Author

Kuzmanović, Nemanja, Puławska, Joanna, Smalla, Kornelia, and Nesme, Xavier

Subjects
AGROBACTERIUM, NUCLEOTIDE sequence, GRAPE genetics, GALLS (Botany), GENOMICS
Abstract

The plant tumorigenic strain NCPPB 1650 T isolated from Rosa × hybrida , 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 DNA–DNA hybridization (DDH) comparisons between strains NCPPB 1650 T 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”. As for other species of the genus Agrobacterium , the major fatty acid of the strains studied was 18:1 w7c (73.42–78.12%). 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 1650 T (=DSM 30203 T = LMG 230 T = CFBP 4470 T = IAM 13558 T = JCM 20915 T ). [ABSTRACT FROM AUTHOR]

Published
2018
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29. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.

Author

Lassalle, Florent, Planel, Rémi, Penel, Simon, Chapulliot, David, Barbe, Valérie, Dubost, Audrey, Calteau, Alexandra, Vallenet, David, Mornico, Damien, Bigot, Thomas, Guéguen, Laurent, Vial, Ludovic, Muller, Daniel, Daubin, Vincent, and Nesme, Xavier

Subjects
HORIZONTAL gene transfer, BACTERIAL genomes, AGROBACTERIUM, BACTERIAL ecology, NUCLEOTIDES
Abstract

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to newecological niches. However, among themany genes acquired throughHGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species.We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutralmodel of transfer, inwhich neighboring geneswould be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches,which consistently hint at a strong selective role of host plant rhizospheres. [ABSTRACT FROM AUTHOR]

Published
2017
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30. Toward an ecological concept for bacterial species in Agrobacterium

Author

Campillo, Tony, Lassalle, Florent, Shams, M., Ramírez-Bahena, Martha Helena, Baude, Jessica, Lavire, Celine, Bertolla, Franck, Muller, Daniel, Chapulliot, David, Bayet, Christine, Guéguen, Laurent, Daubin, Vincent, Hommais, Florence, Nesme, Xavier, Burr, Sally, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie et pharmacogénomique du traitement de la drépanocytose (PHATMAH (U_458 / U_763)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Fractionnement des AgroRessources et Environnement (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de la Recherche Agronomique (INRA), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2010

31. Increasing aggressiveness of the phytopathogenic bacteria Ralstonia solanacearum by gene acquisition : [O1-08, Abstract]

Author

Coupat-Goutaland, Bénédicte, Guidot, Alice, Bernillon, D., Prior, Philippe, Nesme, Xavier, and Bertolla, Franck

Subjects
food and beverages, H20 - Maladies des plantes
Abstract

Ralstonia solanacearum, the causal agent of bacterial wilt disease on many crops including Solanaceae and Musaceae, is a complex of species (i.e. phylotypes). Along to this high diversity, R. solanacearum is also characterized by a high genetic plasticity, both being suspected to be involved in its rapid pathogenic evolution as well as in its large host range (more than 450 plant species). The R. solanacearum genome plasticity is evidenced by the presence of "ACUR" (alternative codon usage region) in their genomes, and by the ability of all species tested up to now to capture and integrate free exogenous DNA from the environment (1). In this context, we studied importance and role of gene transfers and natural transformation for the evolution of the pathogenicity amongst members of the species complex. In this work, we measured frequency and size of genomic regions that can be exchanged during inter-phylotype natural transformations, by analyzing more specifically the mobility of regions containing type Ill effectors or ACUR regions suspected to originate from bacteria other out of the R. solanacearum complex. Extent and number of transfer events were also evaluated by using selective antibiotics markers as well as by comparative genomics with DNA microarrays (2). Transfers of large DNA regions, > 80 kb, were detected between phylotypes, among which 50 kb were gene replacements that induced single nucleotide polymorphisms (SNPs), and 30 kb corresponding to the acquisition of 20 new genes with 3 potentially involved in pathogenicity. In order to determine whether the acquisition of such a region rich in pathogenicity genes could alter the recipient pathogenicity, we then compared tomato responses to inoculation of wild type and transformant strains. Very interestingly, we found that the transformant strain became much more aggressive than its wild parent, suggesting that such inter-species gene transfers may play a great role in the rapid emergence of new pathotypes of R. solanacearum.

Published
2010

32. Involvement of horizontal gene transfer in the emergence of new pathotypes of Ralstonia solanacearum : [Abstract of poster]

Author

Coupat-Goutaland, Bénédicte, Guidot, Alice, Prior, Philippe, Nesme, Xavier, and Bertolla, Franck

Subjects
H20 - Maladies des plantes
Abstract

Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. R. solanacearum has been described as a highly flexible organism capable of counteracting plant resistance, leading to the emergence of a new pathological variant. We propose to investigate the fundamental role of horizontal gene transfer (HGT) in its genome evolution. In the R. solanacearum species complex, the natural ability to transform has been described as an ubiquitous physiological trait. Eighty percent of strains distributed in all phylotypes - likely species - have the ability to acquire free plasmids and/or genomic DNA (Coupat et al., 2008, FEMS Microbiol Ecol 66:14-24). Extent and number of transfer events were also evaluated by using selective antibiotics markers as well as by comparative genomic hybridization with DNA microarrays. Results showed that replacements might involve DNA fragments up to 90 kb and multiple integration events into the R. solanacearum genome. In addition, inter-phylotype HGT studies showed that transformants were able to acquire large DNA blocks (30 kb) containing pathogenicity determinants from the DNA donor (Guidot et al., 2009, ISME J. doi :1038/ismej.2009.14). The natural transformation mechanism thus appears as one of the main forces for the generation of emergent pathogens. We confirmed that a recombinant strain, which was found to be more virulent on tomato than its wild type parental strain, has acquired a type III effector which was not present in the wild type parental genome. (Texte intégral)

Published
2009

33. Homologous recombination in \textitAgrobacterium: potential implications for the genomic species concept in bacteria

Author

Costechareyre, Denis, Bertolla, Franck, Nesme, Xavier, 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), 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]Life Sciences [q-bio]
Published
2009

34. Natural transformation in the Ralstonia solanacearum species complex: numberand size of DNA that can be transferred

Author

Coupat, Bénédicte, Chaumeille-Dole, Fanny, Fall, Saliou, Prior, Philippe, Simonet, Pascal, Nesme, Xavier, Bertolla, Franck, 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), 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), Peuplement Végétaux et Bioagresseurs en Milieu Tropical - Pôle de Protection des Plantes (3P), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), 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)-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 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)-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), 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), Ampère (AMPERE), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-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)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ralstonia solanacearum, food and beverages, horizontal gene transfer, natural transformation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; 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

35. Natural transformation in the Ralstonia solanacearum species complex:numberand size ofDNAthat can be transferred

Author

Coupat , Bénédicte, Chaumeille-Dole , Fanny, Fall , Saliou, Prior , Philippe, Simonet , Pascal, Nesme , Xavier, Bertolla , Franck, 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 ), 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 ), CIRAD-INRA, Pôle de Protection des Plantes (3P), Bios UMR C53, and CIRAD-INRA

Subjects
[ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Ralstonia solanacearum, food and beverages, horizontal gene transfer, natural transformation
Abstract

International audience; 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

36. Reclassification of Xanthomonads associated with anacardiaceae into two species and three pathovars

Author

Ah-You, Nathalie, Gagnevin, Lionel, Grimont, Patrick A. D., Brisse, Sylvain, Nesme, Xavier, Chiroleu, Frédéric, Bui Thi Ngoc, Lan, Jouen, Emmanuel, Lefeuvre, Pierre, Vernière, Christian, and Pruvost, Olivier

Subjects
Xanthomonas, Anacardiaceae, Xanthomonas axonopodis, Taxonomie, Classification, Pathotype, H20 - Maladies des plantes
Abstract

Mango, cashew, Brazilian pepper and ambarella are host species of Xanthomonas strains which have a broad genetic and phenotypic diversity. Until now, it was not determined whether they should be classified as strains of a single pathovar with a broad host range or as several pathovars. A polyphasic approach was used to determine their respective taxonomie positions, their mutual relationships and their relationship to other Xanthomonas species. Pathogenicity tests and amplified fragment length polymorphism (AFLP) suggested the distinction of three pathovars presenting a host specialization: pv mangiferaeindicae on mango and Brazilian pepper, pv. anacardii on cashew and pv. spondiae on ambarella. AFLP and multilocus sequence analysis (MLSA) were congruent and showed that the three pathovars are related to X. axonopodis genetic groups 9.5, 9.6 and 9.4, respectively. DNADNA hybridization, AFLP and MLSA indicated that pvs. mangiferaeindicae, anacardii and citri (the causal agent of citrus canker) belong to a single species and that they should not be classified as X. axonopodis. Our results agree with the recent elevation of pv citri to, species level and propose to include pvs. mangiferaeindicae and anacardii in this species. Pathovar spondiae is genetically related to group 9.4, for which no reclassification has yet been proposed. (Texte intégral)

Published
2008

38. The immobilisation of DNA strands on silica surface by means of chemical grafting

Author

Dugas, Vincent, Chevalier, Yves, Depret, Géraldine, Nesme, Xavier, Souteyrand, Éliane, 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), M. Miguel, H. D. Burrows, 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), Matériaux organiques à propriétés spécifiques (LMOPS), Laboratoire d'Electrochimie et de Physico-chimie des Matériaux et des Interfaces (LEPMI ), Institut de Chimie du CNRS (INC)-Institut National Polytechnique de Grenoble (INPG)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut National Polytechnique de Grenoble (INPG)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie et Fonctionnalisation des Surfaces (IFoS), École Centrale de Lyon (ECL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
Chemical grafting, [SDV]Life Sciences [q-bio], 0206 medical engineering, DNA, [CHIM.MATE]Chemical Sciences/Material chemistry, 02 engineering and technology, 020601 biomedical engineering, 030218 nuclear medicine & medical imaging, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 03 medical and health sciences, 0302 clinical medicine, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Oligonucleotide, DNA chip, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The surface chemistry and physicochemical phenomena involved in the chemical grafting process of short DNA single strands on silica or glass slides has been studied in order to be able to prepare reusable DNA-arrays (DNA-chips) with an optimum signal-to-noise ratio. Some crucial steps of the immobilisation of oligonucleotides on silica surfaces by means of their chemical grafting at their 3' terminus (aminolinker) were studied carefully. A prior grafting of the surface with an organosilane is performed. The surface of the silica should have been completely covered by a dense anionic grafted layer in order to minimise DNA adsorption with respect to chemical grafting and allow an easy desorption of non grafted materials. The efficiency of the covalent immobilisation of DNA strands performed from a very dilute solution in a small volume is drastically increased by means of a slow in situ evaporation of the solvent. The discrimination between covalently bound and adsorbed oligonucleotides requires a correct control of the rinsing processes after the immobilisation reaction. An efficient washing process increases the signal-to-noise ratio. Ready hybridisation of complementary oligonucleotides or large double strands bearing the complementary sequence at their centre (PCR fragments) could be obtained at the surface. A clean and robust immobilisation process allows a clear-cut discrimination between hybridisation and non-specific adsorption and very low levels of background (noise) in the radioactivity measurements. Several cycles of hybridisation and denaturation were carried out. Glass plates functionalised according to the same process might be used for the mass preparation of DNA-arrays.

Published
2004

39. Outils moléculaires pour la caractérisation de bactéries résistantes aux antibiotiques

Author

Aarts, H.J.M., Boumedine, K.S., Nesme, Xavier, Cloeckaert, Axel, Station de Pathologie aviaire et parasitologie [Nouzilly] (PAP), 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), 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.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, health care facilities, manpower, and services, education, health care economics and organizations
Abstract

Mechanisms of resistance to antibiotics in animal and zoonotic pathogens; International audience

Published
2001

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

Author

Pionnat, S., Keller, Harald, Hericher, Delphine, Bettachini, Andree, Dessaux, Yves, Nesme, Xavier, Poncet, C., Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and 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)

Subjects
ROSE, CROWN GALL, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1999

41. Validity, sensitivity and resolution limit of the PCR-RFLP analysis of the rrs (16S rRNA gene) as a tool to identify soil-borne and plant-associated bacterial populations

Author

Oger, Philippe, Dessaux, Yves, Petit, A., Gardan, L., Manceau, Charles, Chomel, C., Nesme, Xavier, Institut des Sciences Végétales, Centre National de la Recherche Scientifique (CNRS), Unité de recherche Pathologie végétale et phytobactériologie, Institut National de la Recherche Agronomique (INRA), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon

Subjects
PCR-RFLP, 16S, [SDV.GEN]Life Sciences [q-bio]/Genetics, AGROBACTERIUM, XANTHOMONAS, PSEUDOMONAS, RRS
Abstract

International audience; The value of the restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified rrs (16S ribosomal ribonucleic acid [rRNA] gene) for the rapid identification of bacteria isolated from soil or plants, and the limits of this technique, were evaluated using bacterial genera characteristic of the above-mentioned ecosystems. Results showed that up to two restriction site differences may occur between rrs operons within the same bacterial genome as well as between bacteria belonging to the same genospecies. In spite of these limited differences, members of the same genospecies yield very similar rrs RFLP patterns. The identification limit varies according to the analyzed taxa. Species can be differentiated amongst members of both the family Rhizobiaceae and the genus Stenotrophomonas, while the technique only allows grouping of closely related species amongst Xanthomonas spp. and amongst species related to Psendomonas syringae. On the basis of their rrs RFLP profiles, all presently known species of Agrobacterium can be routinely identified using only the enzymes HpaII (or MspI), AUIL and HaeIII. Moreover, the method was also found to be valuable in assessing the biodiversity of a bacterial community isolated from the rhizosphere. From the comparison of empiric rrs RFLPs, published sequences and deoxyribonucleic acid (DNA) pairing studies, we suggest that the occurrence of five different restriction sites within two rrs genes is the minimum difference required to clearly establish that two relevant bacteria belong to different genospecies.; L’intérêt et les limites de l’identification bactérienne basée sur l’analyse du gène codant pour l’ARN ribosomique 16S par PCR-RFLP ont été évalués dans plusieurs genres bactériens typiques des écosystèmes sol et plante. Les résultats montrent qu’il peut y avoir jusqu’à deux sites de restriction différents entre les gènes rrs de bactéries appartenant à la même espèce génomique ou entre différents opérons d’un même génome. Les résultats permettent cependant d’identifier les bactéries jusqu’au niveau de l’espèce chez les Rhizobiaceae et chez Stenotrophomonas, et jusqu’au niveau du groupe d’espèces apparentées d’un même genre chez Xanthomonas et dans le groupe apparenté à P. syringae. De plus, la méthode s’est révélée parfaitement adaptée pour identifier et classer les bactéries isolées d’un peuplement rhizosphérique, en permettant une identification approchée du genre, voire de l’espèce. La comparaison des données de PCR-RFLP avec les données de séquences et d’hybridations ADN-ADN suggèrent qu’un minimum de cinq sites de restriction polymorphes dans le gène 16S est nécessaire pour affirmer que des bactéries appartiennent à des espèces génomiques différentes.

Published
1997

42. Impact of the crown gall disease on vigour and yield of rose trees

Author

Poncet, C., Antonini, Chiara, Bettachini, Andree, Hericher, Delphine, Pionnat, S., Dessaux, Yves, Nesme, Xavier, ProdInra, Migration, Station de botanique et de pathologie végétale, Institut National de la Recherche Agronomique (INRA), and Unité de recherche Pathologie végétale et phytobactériologie

Subjects
[SDV] Life Sciences [q-bio], CRAWN GALL, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1996

43. Novel Ti plasmids in Agrobacterium strains isolated from fig tree and chrysanthemum tumors and their opinelike molecules

Author

Vaudequin-Dransart, V., Petit, A., Poncet, C., Ponsonnet, C., Nesme, Xavier, Jones, J.B., Bouzar, H., Chilton, W.S., Dessaux, Yves, Station de botanique et de pathologie végétale, Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], CRAWN GALL, FIGUIER, [SDV]Life Sciences [q-bio], CHRYSANTHEME, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1995

48. Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations.

Author

Mousavi, Seyed Abdollah, Willems, Anne, Nesme, Xavier, de Lajudie, Philippe, and Lindström, Kristina

Subjects
RHIZOBIACEAE, MICROORGANISM phylogeny, RHIZOBIUM, SPECIES, SEQUENCE alignment, AGROBACTERIUM
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. [ABSTRACT FROM AUTHOR]

Published
2015
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49. GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands.

Author

Lassalle, Florent, Périan, Séverine, Bataillon, Thomas, Nesme, Xavier, Duret, Laurent, and Daubin, Vincent

Subjects
BACTERIAL genomes, GENETIC drift, BACTERIAL evolution, BACTERIAL genes, BACTERIAL genetics
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. [ABSTRACT FROM AUTHOR]

Published
2015
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50. Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

Author

Mousavi, Seyed Abdollah, Österman, Janina, Wahlberg, Niklas, Nesme, Xavier, Lavire, Céline, Vial, Ludovic, Paulin, Lars, de Lajudie, Philippe, and Lindström, Kristina

Subjects
RHIZOBIUM, BACTERIA phylogeny, AGROBACTERIUM, RHIZOBIACEAE, PHYTOPATHOGENIC bacteria, NITROGEN-fixing bacteria, TAXONOMY
Abstract

Abstract: 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. [Copyright &y& Elsevier]

Published
2014
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