DOCSLIB.ORG

Curriculum Vitae

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Curriculum Vitae Faculty of Sciences Department of Biochemistry and Microbiology Laboratory of Microbiology Diagnostics for quarantine plant pathogenic Clavibacter and relatives: molecular characterization, identification and epidemiological studies Joanna Załuga Promoter: Prof. Dr. Paul De Vos Co-promoter: Prof. Dr. Martine Maes Dissertation submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) in Sciences, Biotechnology Joanna Załuga – Diagnostics for quarantine plant pathogenic Clavibacter and relatives: molecular characterization, identification and epidemiological studies Copyright ©2013 Joanna Załuga ISBN-number: No part of this thesis protected by its copyright notice may be reproduced or utilized in any form, or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promoters. Printed by University Press | www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. This Ph.D. work was financially supported by a QBOL (Quarantine Barcoding Of Life) project KBBE- 2008-1-4-01 nr 226482 funded under the Seventh Framework Program (FP 7) of the European Union. Publicly defended in Ghent, Belgium, October 11th, 2013 ii Examination Committee Prof. Dr. Savvas Savvides (Chairman) L-Probe: Laboratory for protein Biochemistry and Biomolecular Engineering Faculty of Sciences, Ghent University, Belgium Prof. Dr. Paul De Vos (Promoter) LM-UGent: Laboratory of Microbiology, Faculty of Science, Ghent University, Belgium BCCM-LMG Bacteria Collection, Ghent, Belgium Prof. Dr. Martine Maes (Co-promoter) Plant Sciences Unit – Crop Protection Institute for Agricultural and Fisheries Research (ILVO), Merelbeke, Belgium Dr. Peter Bonants Plant Research International (PRI) Business Unit Biointeractions & Plant Health, Wageningen, The Netherlands Ir. Johan Van Vaerenbergh Plant Sciences Unit – Crop Protection Institute for Agricultural and Fisheries Research (ILVO), Merelbeke, Belgium Dr. Pieter Stragier Laboratory for Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Anne Willems Laboratory for Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Monica Höfte Laboratory of Phytopathology, Department of Crop Protection Faculty of Bioscience Engineering, Ghent University, Belgium Prof. Dr. Peter Dawyndt Department of Applied Mathematics, Computer Science and Statistics PC-Lab of the Faculty of Science, Ghent University, Belgium iii Acknowledgements-Podziękowania To start I wish to thank prof. Dr. Paul De Vos who gave me the opportunity to carry out the PhD in the Laboratory of Microbiology. Your guidance, thoughtful insights and support were very important at every stage of my work. I am thankful that I could count on you, especially during the last few, very intensive months of my PhD. Your encouragement, advices and suggestions were invaluable for completing this work. I am grateful to the examination committee for their helpful suggestions, constructive remarks and fruitful discussions that helped me to improve my thesis. Prof. Dr. Martine Maes, thank you for your advice and comments on my publications and thesis. Dr. Peter Bonants, Prof. dr. Monica Höfte, Ir. Johan Van Vaerenbergh and dr. Pieter Stragier, thank you very much for taking your time to read my PhD and for your positive feedback. Kim, although you supervised me only at the beginning it was the most important time for me and I am thankful that I could work with you. Your wide knowledge and scientific input greatly influenced my first steps in the exciting scientific world. Writing the first article is never easy but with your guidance and support it was one of the most important and unforgettable experiences for me. I am grateful not only for your great scientific supervision and what you taught me during these four years but also for being a great colleague! Dear Johan, I would like to thank you very, very much for these four years. It was a great experience to work with you. I am grateful for showing me the real diagnostic lab, for all our discussions and for a wonderful time in ILVO. My dearest colleagues, Sven, Ines, Jonas and Bram, I spent with you the best time in the lab. You were the best company I could imagine to have during my PhD. Our coffee breaks discussions, Friday lunches, common conferences, meetings and practical exercises, I could not think of anyone better to share these great moments with. Sven, our philosopher and discussion man, thanks for all our chats and laughs and for being a super friend. Jonas, our potato/dj man, the most optimistic person I know, it was great to have someone so positive in the office. Ines, my best desk mate, thanks for your help at the beginning, for all the translations from Dutch, your support and the great moments we had together. Bram, the youngest in our team, hopping around, never tired and always full of ideas. Thanks for all the fun we had in the PDV group. Margo, you are an amazing person who has so much positive energy and who is always ready to help others. I will never forget your support and help, especially at the beginning of my adventure in LM-UGent and during my Erasmus exchange. Thank you for everything! Bart, Liesbeth, Joke, Evie, thanks for always answering my questions and for assistance in performing experiments in the lab. I would like to thank all colleagues from the Laboratory of Microbiology and from ILVO for creating a friendly atmosphere and for your enthusiastic support. It was a pleasure to work in such a nice environment. v I cannot forget my best friend Kamila who shared with me good and bad moments, who always was there when I needed her. Without you I would never be where I am now. I still remember our first days in Ghent when we started together. New places, new people, new challenges and even though it was tough we did it! Dzięki za wszystko moja najlepsza koleżanko! My friends, Kasie, Agi, Asie, Anie, Radek, Agata, Mati, Linda, Giacomo, Edyta, Marta, Lidka and many others I have always a wonderful time with you. Our parties, Friday drinks and chats are unforgettable moments. I am happy I met such great people! Moi Rodzice, Aga i Paweł, dziękuję Wam za dodawanie mi otuchy i wiarę we mnie. Dziękuję za to, że zawsze ciepło mnie witaliście kiedy wracałam do rodzinnego domu. Mamo, tato, wiem, że przyjazd do Belgii to dla Was duże przeżycie, tym bardziej dziękuję za to, że sie zdecydowaliście. Ik wil graag de familie van Stan bedanken, vooral Annick en Filip, ik heb veel steun van jullie gekregen. Jullie hebben me heel warm ontvangen. Ik dank jullie hartelijk voor jullie gastvrijheid, interesse en vriendschap. Stan, moje Kochanie, I want to thank you for your support, understanding and for being there for me. I am really happy that I met you that evening at Brahim’s. You always believed in me and tried to encourage me during hard times. Dziękuję for all the wonderful days we had, all the great moments we have now and I am looking forward to the future with you! Merci! Bedankt! Dziękuję! Thank you! vi List of abbreviations ACN Acetonitrile ATCC American Type Culture Collection BCCM Belgian Coordinated Collections of Micro-organisms BOX-PCR BOX-A1R-based repetitive extragenic palindromic-PCR BLAST Basic Local Alignment Search Tool CDS Coding DNA Sequence CFBP Collection Française de Bactéries associées aux Plantes CHCA α-cyano-4-hydroxycinnamic acid Cmi Clavibacter michiganensis subsp. insidiosus Cmm Clavibacter michiganensis subsp. michiganensis Cmn Clavibacter michiganensis subsp. nebraskensis Cms Clavibacter michiganensis subsp. sepedonicus Cmt Clavibacter michiganensis subsp. tessellarius CMR Comprehensive Microbial Resource CRISPR Clustered Regularly Interspaced Short Palindromic Repeats CWDE Cell Wall Degrading Enzyme dpi days post inoculation DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen EDGAR Efficient Database framework for comparative Genome Analyses using BLAST score Ratios EDTA Ethylene Diamine Tetraacetic Acid ELISA Enzyme-Linked Immunosorbent Assay EPPO European and Mediterranean Plant Protection Organization EPS Extracellular Polysaccharide ERIC-PCR Enterobacterial Repetitive Intergenic Consensus-PCR EU European Union FAME Fatty Acid Methyl Esters FAO Food and Agriculture Organization of the United Nations HGDI Hunter-Gaston Diversity Index HGT Horizontal Gene Transfer HR Hypersensitive Response ILVO Instituut voor Landbouw- en VisserijOnderzoek IS Insertion Sequence IS-LM-PCR Insertion Sequence Ligation-Mediated PCR ISF International Seed Federation ISSR Inter-Simple Sequence Repeat ITS Internal Transcribed Spacer region LMG Laboratory for Microbiology Ghent MALDI-TOF MS Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry MCL Maximum Composite Likelihood model MEGA Molecular Evolutionary Genetics Analysis software ML Maximum Likelihood MLST Multi Locus Sequence Typing MLVA Multilocus Variable-Number Tandem Repeats Analysis vii MP Mate-Paired MP Maximum Parsimony MST Minimum Spanning Tree MTNA Mannitol, Trimethoprim, Nalidixic acid, Amphotericin medium NCBI National Centre for Biotechnology Information NCPPB National Collection of Plant Pathogenic Bacteria NJ Neighbor-Joining OEPP Organisation Européenne et Méditerranéenne pour la Protection des Plantes PAI Pathogenicity Island PAMPs Pathogen-Associated Molecular Patterns PCR Polymerase Chain Reaction NVWA Bacterial collection (Wageningen, The Netherlands) PDDCC Plant Diseases Division Culture Collection PE
Load more

Recommended publications
  • Corynebacterium Sp.|NML98-0116
    1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album
    [Show full text]
  • Evolutionary Genomics of Conjugative Elements and Integrons
    Université Paris Descartes École doctorale Interdisciplinaire Européenne 474 Frontières du Vivant Microbial Evolutionary Genomic, Pasteur Institute Evolutionary genomics of conjugative elements and integrons Thèse de doctorat en Biologie Interdisciplinaire Présentée par Jean Cury Pour obtenir le grade de Docteur de l’Université Paris Descartes Sous la direction de Eduardo Rocha Soutenue publiquement le 17 Novembre 2017, devant un jury composé de: Claudine MÉDIGUE Rapporteure CNRS, Genoscope, Évry Marie-Cécile PLOY Rapporteure Université de Limoges Érick DENAMUR Examinateur Université Paris Diderot, Paris Philippe LOPEZ Examinateur Université Pierre et Marie Curie, Paris Alan GROSSMAN Examinateur MIT, Cambdridge, USA Eduardo ROCHA Directeur de thèse CNRS, Institut Pasteur, Paris ِ عمحمود ُبدرويش َالنرد َم ْن انا ِٔ َقول ُلك ْم ما ا ُقول ُلك ْم ؟ وانا لم أ ُك ْن َ َج ًرا َص َق َل ْت ُه ُالمياه َفأ ْص َب َح ِوهاً و َق َصباً َثق َب ْت ُه ُالرياح َفأ ْص َب َح ًنايا ... انا ِع ُب َالن ْرد ، ا َرب ُح يناً وا َس ُر يناً انا ِم ُثل ُك ْم ا وا قل قليً ... The dice player Mahmoud Darwish Who am I to say to you what I am saying to you? I was not a stone polished by water and became a face nor was I a cane punctured by the wind and became a lute… I am a dice player, Sometimes I win and sometimes I lose I am like you or slightly less… Contents Acknowledgments 7 Preamble 9 I Introduction 11 1 Background for friends and family . 13 2 Horizontal Gene Transfer (HGT) . 16 2.1 Mechanisms of horizontal gene transfer .
    [Show full text]
  • Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter Baumannii
    UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR IV TESIS DOCTORAL Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter baumannii Análisis Epidemiológico y Molecular de la Virulencia y la Antibiorresistencia en Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh DIRECTORA Mónica Suárez Rodríguez Madrid, 2017 © Elias Dahdouh, 2016 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA DEPARTAMENTO DE BIOQUIMICA Y BIOLOGIA MOLECULAR IV TESIS DOCTORAL Análisis Epidemiológico y Molecular de la Virulencia y la Antibiorresistencia en Acinetobacter baumannii Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh Directora Mónica Suárez Rodríguez Madrid, 2016 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA Departamento de Bioquímica y Biología Molecular IV ANALYSIS EPIDEMIOLOGICO Y MOLECULAR DE LA VIRULENCIA Y LA ANTIBIORRESISTENCIA EN Acinetobacter baumannii EPIDEMIOLOGICAL AND MOLECULAR ANALYSIS OF VIRULENCE AND ANTIBIOTIC RESISTANCE IN Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh Bajo la dirección de la doctora Mónica Suárez Rodríguez Madrid, Diciembre de 2016 First and foremost, I would like to thank God for the continued strength and determination that He has given me. I would also like to thank my father Abdo, my brother Charbel, my fiancée, Marisa, and all my friends for their endless support and for standing by me at all times. Moreover, I would like to thank Dra. Monica Suarez Rodriguez and Dr. Ziad Daoud for giving me the opportunity to complete this doctoral study and for their guidance, encouragement, and friendship.
    [Show full text]
  • High-Quality Draft Genome Sequence of Curtobacterium Sp. Strain Ferrero
    PROKARYOTES crossm High-Quality Draft Genome Sequence of Curtobacterium sp. Strain Ferrero Ebrahim Osdaghi,a,b Natalia Forero Serna,a* Stephanie Bolot,c,d Marion Fischer-Le Saux,e Marie-Agnès Jacques,e Perrine Portier,e,f Sébastien Carrère,c,d Ralf Koebnika Downloaded from IRD, Cirad, Université de Montpellier, IPME, Montpellier, Francea; Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iranb; INRA, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 441, Castanet-Tolosan, Francec; CNRS, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 2594, Castanet-Tolosan, Franced; INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, Francee; CIRM-CFBP, French Collection for Plant-Associated Bacteria, INRA, IRHS, Angers, Francef ABSTRACT Here, we present the high-quality draft genome sequence of Curto- bacterium sp. strain Ferrero, an actinobacterium belonging to a novel species iso- Received 3 November 2017 Accepted 6 http://mra.asm.org/ November 2017 Published 30 November lated as an environmental contaminant in a bacterial cell culture. The assembled 2017 genome of 3,694,888 bp in 49 contigs has a GϩC content of 71.6% and contains Citation Osdaghi E, Forero Serna N, Bolot S, 3,516 predicted genes. Fischer-Le Saux M, Jacques M-A, Portier P, Carrère S, Koebnik R. 2017. High-quality draft genome sequence of Curtobacterium sp. strain Ferrero. Genome Announc 5:e01378-17. he genus Curtobacterium comprises Gram-positive aerobic corynebacteria (family https://doi.org/10.1128/genomeA.01378-17. TMicrobacteriaceae, order Actinomycetales), including at least 11 well-defined species Copyright © 2017 Osdaghi et al.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Adaptive Differentiation and Rapid Evolution of a Soil Bacterium Along a Climate Gradient
    Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient Alexander B. Chasea,b,1, Claudia Weihea, and Jennifer B. H. Martinya aDepartment of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697; and bCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved March 30, 2021 (received for review January 29, 2021) Microbial community responses to environmental change are largely shifts are due to adaptive differentiation among taxa as a result associated with ecological processes; however, the potential for of past evolutionary divergence. Concurrently, the same selective microbes to rapidly evolve and adapt remains relatively unexplored forces can also shift the abundance of conspecific strains and in natural environments. To assess how ecological and evolutionary alter the allele frequencies of preexisting genetic variation, which processes simultaneously alter the genetic diversity of a microbiome, at this genetic scale is defined as an evolutionary process (14). we conducted two concurrent experiments in the leaf litter layer of Finally, evolution through de novo mutation can provide a new soil over 18 mo across a climate gradient in Southern California. In the source of genetic variation that may allow for further adaptation first experiment, we reciprocally transplanted microbial communities to environmental change. from five sites to test whether ecological shifts in ecotypes of the In this study, we aimed to capture this continuum of ecological abundant bacterium, Curtobacterium, corresponded to past adaptive and evolutionary processes that together produce the response differentiation.
    [Show full text]
  • Supplement of Screening of Cloud Microorganisms Isolated at the Puy De Dôme (France) Station for the Production of Biosurfactants
    Supplement of Atmos. Chem. Phys., 16, 12347–12358, 2016 http://www.atmos-chem-phys.net/16/12347/2016/ doi:10.5194/acp-16-12347-2016-supplement © Author(s) 2016. CC Attribution 3.0 License. Supplement of Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants Pascal Renard et al. Correspondence to: Anne-Marie Delort ([email protected]) The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence. Table S1. Strains are isolated during 39 cloud events (from 2004 to 2014) gathered in four categories according to the physicochemical characteristics of the cloud waters (Blue: marine, purple: highly marine, green: continental and black: polluted) as described by Deguillaume et al. (2014). Cloud Nb of Ions (µM) Composition Date pH 2- - - + + 2+ + 2+ Event strains SO 4 NO 3 Cl Acetate Formate Oxalate Succinate Malonate Na NH 4 Mg K Ca 21 Marine 2 2004-01 5.6 NA NA NA NA NA NA NA NA NA NA NA NA NA 23 Polluted 2 2004-02 3.1 NA NA NA NA NA NA NA NA NA NA NA NA NA 29 Marine 1 2004-07 5.5 NA NA NA NA NA NA NA NA NA NA NA NA NA 30 Marine 3 2004-09 7.6 3.8 6.5 12.0 6.0 6.0 0.5 0.1 0.16 19.4 54.9 4.9 4.1 12.0 32 Continental 1 2004-12 5.5 72.1 95.8 31.5 0.0 0.3 0.3 0.1 0.17 74.4 132.4 7.6 9.0 73.7 42 Continental 25 2007-12 4.7 39.7 198.4 20.2 10.2 5.8 2.9 0.6 0.58 19.1 148.2 3.5 11.9 58.0 43 Highly marine 25 2008-01 5.9 9.4 21.4 81.4 11.4 6.7 1.2 0.2 0.28 315.7 35.9 11.8 13.7 26.0 44 Continental 14 2008-02 5.2 24.6 65.9 17.2 26.8 18.0 1.3 0.5 0.39
    [Show full text]
  • Soil Ecotypes Along a Climate Gradient
    Emergence of Soil Bacterial Ecotypes Along a Climate Gradient Alexander B. Chase1#, Zulema Gomez-Lunar2, Alberto E. Lopez1, Junhui Li2, Steven D. Allison1,2, Adam C. Martiny1,2, and Jennifer B.H. Martiny1 1Department of Ecology and Evolutionary Biology, University of California, Irvine, California 2Department of Earth System Sciences, University of California, Irvine, California #Address correspondence to: Alexander B. Chase, [email protected] 3300 Biological Sciences III Department of Ecology and Evolutionary Biology University of California Irvine, CA 92697 Running Title: Soil ecotypes along a climate gradient Article Accepted Thi s article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1462-2920.14405 This article is protected by copyright. All rights reserved. Originality-Significance Statement Microbial community analyses typically rely on delineating operational taxonomic units; however, a great deal of genomic and phenotypic diversity occurs within these taxonomic groupings. Previous work in closely-related marine bacteria demonstrates that fine-scale genetic variation is linked to variation in ecological niches. In this study, we present similar evidence for soil bacteria. We find that an abundant and widespread soil taxon encompasses distinct ecological populations, or ecotypes, as defined by their phenotypic traits. We further validated that differences in these soil ecotypes correspond to variation in their distribution across a regional climate gradient. Thus, there exists genomic and phenotypic diversity within this soil taxon that contributes to niche differentiation.
    [Show full text]
  • Rathayibacter Rathayi Comb , Nov,, Rathayibacter Tritici Comb , Nov,, Rathayibacter Iranicus Comb, Nov., and Six Strains from Annual Grasses H
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1993, p. 143-149 Vol. 43, No. 1 0020-7713/93/010143-07$02.00/0 Copyright 0 1993, International Union of Microbiological Societies Rathayibacter gen, nov., Including the Species Rathayibacter rathayi comb , nov,, Rathayibacter tritici comb , nov,, Rathayibacter iranicus comb, nov., and Six Strains from Annual Grasses H. I. ZGURSKAYA, L. I. EVTUSHENKO," V. N. AKIMOV, AND L. V. KALAKOUTSKII All-Russian Collection of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142292, Russia A new genus, Ruthuyibucter, is proposed to accommodate three species of gram-positive, aerobic, coryneform bacteria previously placed in the genus Clavibucter (Ruthuyibucter ruthuyi comb. nov., Ruthuyibucter tritici comb. nov., and Ruthuyibucter irunicus comb. nov.), as well as six strains that were isolated from annual cereal grasses, may be responsible for ryegrass toxicity, and are very similar to the recently described organism Chvibacter toxicus sp. nov. (I. T. Riley and K. M. Ophel, Int. J. Syst. Bacteriol. 42:64-68, 1992). The properties of members of the genus Ruthuyibacter include coryneform morphology, peptidoglycan based on 2,4-diaminobutyric acid (type B2y), predominant menaquinones of the MK-10 type, and phosphatidylglycerol and diphosphatidylglycerol as basic polar lipids. The DNA base compositions range from 63 to 72 mol% G+C. The members of the new genus form a phenetic cluster distinct from Clavibucter spp. at a level
    [Show full text]
  • Coffee Microbiota and Its Potential Use in Sustainable Crop Management. a Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois
    Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois To cite this version: Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois. Coffee Mi- crobiota and Its Potential Use in Sustainable Crop Management. A Review. Frontiers in Sustainable Food Systems, Frontiers Media, 2020, 4, 10.3389/fsufs.2020.607935. hal-03045648 HAL Id: hal-03045648 https://hal.inrae.fr/hal-03045648 Submitted on 8 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License REVIEW published: 03 December 2020 doi: 10.3389/fsufs.2020.607935 Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Benoit Duong 1,2, Pierre Marraccini 2,3, Jean-Luc Maeght 4,5, Philippe Vaast 6, Michel Lebrun 1,2 and Robin Duponnois 1* 1 LSTM, Univ. Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France, 2 LMI RICE-2, Univ. Montpellier, IRD, CIRAD, AGI, USTH, Hanoi, Vietnam, 3 IPME, Univ. Montpellier, CIRAD, IRD, Montpellier, France, 4 AMAP, Univ. Montpellier, IRD, CIRAD, INRAE, CNRS, Montpellier, France, 5 Sorbonne Université, UPEC, CNRS, IRD, INRA, Institut d’Écologie et des Sciences de l’Environnement, IESS, Bondy, France, 6 Eco&Sols, Univ.
    [Show full text]
  • Curtobacterium Flaccumfaciens Pv. Flaccumfaciens Not Detected No
    European and Mediterranean Plant Protection Organization PM 7/102 (1) Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes Diagnostics Diagnostic Curtobacterium flaccumfaciens pv. flaccumfaciens Specific scope Specific approval and amendment This standard describes a diagnostic protocol for Curtobacterium Approved in 2011-09. flaccumfaciens pv. flaccumfaciens.1 of pathogenicity. A flow diagram describing the procedure is Introduction giveninFig.1. Curtobacterium flaccumfaciens pv. flaccumfaciens is the causal agent of the bacterial wilt disease of Phaseolus spp. and is a sys- Identity temic bacterium. The disease was first discovered in the United States (South Dakota) in the 1920s on Phaseolus vulgaris and sub- Name: Curtobacterium flaccumfaciens pv. flaccumfaciens sequently recorded in Australia, Canada, Mexico, South America (Hedges) Collins & Jones. and Tunisia. It has a restricted distributioninRomaniaandRussia. Synonyms:ex-Corynebacterium flaccumfaciens subsp. flaccum- Although it has been recorded in Belgium, Bulgaria, Greece, Hun- faciens (Hedges) Dowson. gary, Poland, Turkey and Ukraine, it has not established and is Taxonomic position: Actinobacteria, Actinomycetales, now considered absent from these countries. It has recently been Microbacteriaceae, Curtobacterium. reported in few fields in South-Eastern Spain (Gonza´lez et al., Notes on taxonomy and nomenclature: In addition to Curto- 2005). Apart from this record, there are few recent records of bacterium flaccumfaciens pv. flaccumfaciens and according to C. flaccumfaciens pv. flaccumfaciens in the EPPO region. the most recent classification (Collins & Jones, 1984; Young No effective chemical methods are known against this disease; et al., 1996, 2004), the species C. flaccumfaciens includes the as C. flaccumfaciens pv. flaccumfaciens is a seed-borne bacte- following pathovars: betae (Cfb), oortii (Cfo), poinsettiae (Cfp) rium, current control methods are based mainly on the use of and ilicis (Cfi).
    [Show full text]
  • Identification, Molecular Epidemiology, and Antibiotic Resistance Characterization of Acinetobacter Spp
    FACULTY OF HEALTH SCIENCES DEPARTMENT OF MEDICAL BIOLOGY UNIVERSITY HOSPITAL OF NORTH NORWAY DEPARTMENT OF MICROBIOLOGY AND INFECTION CONTROL REFERENCE CENTRE FOR DETECTION OF ANTIMICROBIAL RESISTANCE Identification, molecular epidemiology, and antibiotic resistance characterization of Acinetobacter spp. clinical isolates Nabil Karah A dissertation for the degree of Philosophiae Doctor June 2011 Acknowledgments The work presented in this thesis has been carried out between January 2009 and September 2011 at the Reference Centre for Detection of Antimicrobial Resistance (K-res), Department of Microbiology and Infection Control, University Hospital of North Norway (UNN); and the Research Group for Host–Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø (UIT), Tromsø, Norway. I would like to express my deep and truthful acknowledgment to my main supervisor Ørjan Samuelsen. His understanding and encouraging supervision played a major role in the success of every experiment of my PhD project. Dear Ørjan, I am certainly very thankful for your indispensible contribution in all the four manuscripts. I am also very grateful to your comments, suggestions, and corrections on the present thesis. I am sincerely grateful to my co-supervisor Arnfinn Sundsfjord for his important contribution not only in my MSc study and my PhD study but also in my entire career as a “Medical Microbiologist”. I would also thank you Arnfinn for your nonstop support during my stay in Tromsø at a personal level. My sincere thanks are due to co-supervisors Kristin Hegstad and Gunnar Skov Simonsen for the valuable advice, productive comments, and friendly support. I would like to thank co-authors Christian G.
    [Show full text]