Procesos Microbianos
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Chapter 1-General Introduction
Tuscia University Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE) XXVI Cycle of Doctorate in Plant Protection In collaboration with INRA Institute of Avignon, France, Department of Plant Pathology Thesis: Importance of environmental habitats as a reservoir of phytopathogenic bacteria and their role in the evolution of pathogenicity traits AGR/12 By: Dott. Claudia Bartoli Coordinator and Supervisor: Assistant supervisor Prof. Leonardo Varvaro Dott. Cindy E. Morris Signature Signature Dott. Giorgio M. Balestra Signature Defended on: Monday 30 June 2014 Thesis Committee Prof. Laura Mugnai Dr. Elena Di Mattia Prof. Kubilay Kurtulus Bastas Referee Prof. Matthieu Arlat Prof. Gonçalo Almeida Importance of environmental habitats as a reservoir of phytopathogenic bacteria and their role in the evolution of pathogenicity traits Claudia Bartoli Thesis Submitted in partial fulfilment of requirements for the degree of Doctor of Philosophy in Plant Protection at Tuscia University by the authority of the Rector Magnificus Prof. Alessandro Ruggieri In the presence of the Thesis committed appointed by the Doctorate Board To be defended in public On Monday 30 June 2014 Ai miei ragazzacci Himal and Jay Ram Fidelity is the faithful driver Microbes depend on good housekeeping They thrive, survive and flourish Yet new forms appear Confounding the scientist Woe to the status quo . David Sands Contents Chapter 1- General Introduction...................................................................................1 Chapter 2 - Methyl-directed mismatch repair: a mechanism underlying emergence of pathogenic bacteria...................................................................................7 Chapter 3 - A user’s guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.........................25 Chapter 4 - The Pseudomonas viridiflava phylogroups in the P. -
Characterization of Chemosensing in the Alphaproteobacterium <I> Azospirillum Brasilense </I>
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2012 Characterization of Chemosensing in the Alphaproteobacterium Azospirillum brasilense Matthew Hamilton Russell University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Organismal Biological Physiology Commons Recommended Citation Russell, Matthew Hamilton, "Characterization of Chemosensing in the Alphaproteobacterium Azospirillum brasilense . " PhD diss., University of Tennessee, 2012. https://trace.tennessee.edu/utk_graddiss/1469 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Matthew Hamilton Russell entitled "Characterization of Chemosensing in the Alphaproteobacterium Azospirillum brasilense ." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Biochemistry and Cellular and Molecular Biology. Gladys M. Alexandre, Major Professor We have read this dissertation and recommend its acceptance: Dan Roberts, Andreas Nebenfuehr, Erik Zinser Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Characterization of the chemosensory abilities of the alphaproteobacterium Azospirillum brasilense A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Matthew Hamilton Russell August 2012 ii Copyright © 2012 by Matthew Russell All rights reserved. -
Complete Genome Sequence of the Nitrogen-Fixing Bacterium Azospirillum Humicireducens Type Strain Sgz-5T
Yu et al. Standards in Genomic Sciences (2018) 13:28 https://doi.org/10.1186/s40793-018-0322-2 SHORT GENOME REPORT Open Access Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T Zhen Yu1, Guiqin Yang1, Xiaoming Liu1, Yueqiang Wang1, Li Zhuang2* and Shungui Zhou3 Abstract The Azospirillum humicireducens strain SgZ-5T, belonging to the Order Rhodospirillales and the Family Rhodospirillaceae, was isolated from a microbial fuel cell inoculated with paddy soil. A previous work has shown that strain SgZ-5T was able to fix atmospheric nitrogen involved in plant growth promotion. Here we present the complete genome of A. humicireducens SgZ-5T, which consists of a circular chromosome and six plasmids with the total genome size of 6,834,379 bp and the average GC content of 67.55%. Genome annotations predicted 5969 protein coding and 85 RNA genes including 14 rRNA and 67 tRNA genes. By genomic analysis, we identified a complete set of genes that is potentially involved in nitrogen fixation and its regulation. This genome also harbors numerous genes that are likely responsible for phytohormones production. We anticipate that the A. humicireducens SgZ-5T genome will contribute insights into plant growth promoting properties of Azospirillum strains. Keywords: Azospirillum humicireducens, Complete genome, Nitrogen fixation, PGPP Introduction report [11], the nitrogen-fixing capability of strain Bacteria that live in the plant rhizosphere and possess a SgZ-5T was confirmed by acetylene-reduction assay and large array of potential mechanisms to enhance plant identification of a nifH gene. Furthermore, this strain growth are considered as PGPR [1–3]. -
The Rhizobiome of Vachellia (Acacia) Woodlands Surrounding Witwatersrand Gold and Uranium Mine Tailings
The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings Michelle Toni Buck A Thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment for the degree of Doctor of Philosophy Declaration I, Michelle Toni Buck (Person number: 322062), am a student registered for the degree of Doctor of Philosophy (PhD) in the academic year 2018. I hereby declare the following: I am aware that plagiarism (the use of someone else‟s work without their permission and/or without acknowledging the original source) is wrong. I confirm that the work submitted for assessment for the above degree is my own unaided work except where I have explicitly indicated otherwise and acknowledged. In this context, I understand that the use of editing services is considered airded work and must be declared. I have not submitted this work before for any other degree or examination at this or any other University. The informationing used in the Thesis HAS NOT been obtained by me while employed by, or working under the aegis of, any person or organization other than the University. I have followed the required conventions in referencing the thoughts and ideas of others. I understand that the University of the Witwatersrand may take disciplinary action against me if there is a belief that this is not my own unaided work or that I have failed to acknowledge the source of the ideas or words in my writing Signature: Date: 8th August 2018 i Abstract Phytoremediation of mine tailings and surrounding areas provide the most cost-effective means of alleviating their pollutant effects. -
Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES .............................................................................................................................. -
Genomic Insights Into the Versatility of the Plant Growth-Promoting Bacterium Azospirillum Amazonense
Sant’Anna et al. BMC Genomics 2011, 12:409 http://www.biomedcentral.com/1471-2164/12/409 RESEARCHARTICLE Open Access Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense Fernando H Sant’Anna1, Luiz GP Almeida2, Ricardo Cecagno1, Luciano A Reolon1, Franciele M Siqueira1, Maicon RS Machado1, Ana TR Vasconcelos2 and Irene S Schrank1,3* Abstract Background: The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of information on its physiology. In this work, we present a comprehensive analysis of the genomic features of this species. Results: Genes of A. amazonense related to nitrogen/carbon metabolism, energy production, phytohormone production, transport, quorum sensing, antibiotic resistance, chemotaxis/motility and bacteriophytochrome biosynthesis were identified. Noteworthy genes were the nitrogen fixation genes and the nitrilase gene, which could be directly implicated in plant growth promotion, and the carbon fixation genes, which had previously been poorly investigated in this genus. One important finding was that some A. amazonense genes, like the nitrogenase genes and RubisCO genes, were closer phylogenetically to Rhizobiales members than to species of its own order. Conclusion: The species A. amazonense presents a versatile repertoire of genes crucial for its plant-associated lifestyle. Background most research efforts have been dedicated to the species The genus Azospirillum (a-proteobacteria class) encom- Azospirillum brasilense, neglecting the potential offered passes free-living bacteria that can improve the growth by the biological diversity of this genus. of many economically important plants, mainly cereals The bacterium A. -
Unit- VII Microbes in Human Welfare: Silage Production, Biofertilizres, Biopesticides, Biofuel Production and Biodegradation of Agro-Waste
Unit- VII Microbes in human welfare: Silage production, biofertilizres, biopesticides, biofuel production and biodegradation of agro-waste Composting Composting is the controlled biological decomposition of organic matter under aerobic conditions. Organic matter decays naturally, but slowly. Composting involves human intervention to speed up the decay process by manipulating various materials and conditions. Composting is one form of recycling. Organic, compostable material comprises 68% of MSW (Municipal Solid Waste). Most communities can implement some form of composting in order to reduce the amount of waste going into their landfills. Compost can be used in many ways. It can improve soil conditions and plant growth, and reduce the potential for erosion, runoff and non-point source pollution. Compost has also been found to be useful as a medium in plant disease suppression and in biofiltration. Through these uses, compost can be used to remediate or prevent the pollution of soil and groundwater systems. With the time–temperature course, the composting process can be divided into 4 phases: 1. During the first phase a diverse population of mesophilic bacteria and fungi proliferates, degrading primarily the readily available nutrients and thereby raising the temperature to about 45°C. At this point their activities cease, the vegetative cells and hyphae die and eventually lyse, and only heat resistant spores survive. 2. After a short lag period (not always discernible) there occurs a second more or less steep rise of temperature. This second phase is characterized by the development of a thermophilic microbial population comprising some bacterial species, actinomycetes and fungi. The temperature optimum of these microor microorganisms is between 50 and 65°C, their activities terminate at 70–80°C. -
A Taxonomic Study of the Spirillum Lipoferum Group, with Descriptions of a New Genus, Azospirillum Gen. Nov. and Two Species, Azospirillum Lipoferum (Beijerinck) Comb
A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. JEFFREYJ. TARRANDAND NOELR. KRIEC Deptrr/ttrrti/ c!j'Biolo,yy. Virgitlitr Poly/echtric Itls/i/ri/ecitltl S/tr/e Utliversi~y,Bltrckshrrrg, VA, U.S.A. 24061 AND JOHANNADOBEREINER Gtrpre.slr Brtrsilcirrr rle Pe.rtlrriscr Agrop~,crrriritr,Ktn 47, 23460 Serop&tlictr, Rio tle Jtrtleiro, Brnzil Accepted April 25, 1978 TALIRAND,J. J., N. R. KRIEG,and J. DOBEREINER.1978. A taxonomic study of the Spirillirttr lipqf'c,rrittzgroup, with descriptions of a new genus, Azo.spirillrrttr gen. nov. and' two species, Azo.spirillrrttr Iipofi,rrrtt~(Bederinck) comb. nov. and Azo.spirillrtt~~hrosil(,t~.r.e sp. nov. Can. J. Microbiol. 24: 967-980. Sixty-one strains of the root-associated nitrogen fixer Spirillrrtn lipyfi~rrittr exhibited a similar morphology in peptone - succinate salts medium: vibrioid cells having a diametel- of I.Okm. When grown in broth the cells had a single polar flagellum. but when grown on agar at 30°C lateral flagella of shorter wavelength were also formed. The DNA base composition was 69-71 mol % guanine + cytosine when determined by thermal denaturation. DNA homology experiments indicated the occurrence of two distinct but related homology groups: 46 strains were in group I and 15 strains were in group 11. Group I1 strains were distinguished by their ability to use glucose as n sole carbon source fo~.growth in nitrogen-free medium, by their production of an acidic reaction in a peptone-based glucose medium, by their requirement for biotin, and by their formation of wider. -
Molecular Identification of Azospirillum Spp.: Limitations of 16S Rrna and Qualities of Rpod As Genetic Markers
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/310467402 Molecular identification of Azospirillum spp.: Limitations of 16S rRNA and qualities of rpoD as genetic markers Article in Microbiological Research · November 2016 DOI: 10.1016/j.micres.2016.11.009 CITATIONS READS 0 131 4 authors, including: Guillermo Andrés Maroniche Julia Garcia Universidad Nacional de Mar del Plata Instituto Nacional de Tecnología Agropecuaria 30 PUBLICATIONS 146 CITATIONS 4 PUBLICATIONS 1 CITATION SEE PROFILE SEE PROFILE Cecilia Creus Universidad Nacional de Mar del Plata 33 PUBLICATIONS 757 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: ANALISIS ESTRUCTURAL, FISIOLOGICO Y MOLECULAR DE BIOFILMS DE AZOSPIRILLUM SIMPLES Y MIXTOS EN INTERACCION CON PSEUDOMONAS View project “Rol de las auxinas y óxido nítrico producidos por la bacteria Azospirillum brasilense Sp245 en la promoción del crecimiento de microalgas oleaginosas de interés agrobiotecnológico View project All content following this page was uploaded by Guillermo Andrés Maroniche on 24 November 2016. The user has requested enhancement of the downloaded file. Microbiological Research 195 (2017) 1–10 Contents lists available at ScienceDirect Microbiological Research journal homepage: www.elsevier.com/locate/micres Molecular identification of Azospirillum spp.: Limitations of 16S rRNA and qualities of rpoD as genetic markers a,b,∗ c a,b b Guillermo A. Maroniche , Julia E. García , Florencia -
Phytostimulation Du Maïs Par La Bactérie Azospirillum Lipoferum CRT1 : Impact Sur Des Communautés Fonctionnelles Du Microbiote Racinaire Sebastien Renoud
Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : impact sur des communautés fonctionnelles du microbiote racinaire Sebastien Renoud To cite this version: Sebastien Renoud. Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : impact sur des communautés fonctionnelles du microbiote racinaire. Ecologie, Environnement. Université de Lyon, 2016. Français. NNT : 2016LYSE1143. tel-01433755 HAL Id: tel-01433755 https://tel.archives-ouvertes.fr/tel-01433755 Submitted on 13 Jan 2017 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. THESE DE DOCTORAT DE L’UNIVERSITE DE LYON opérée au sein de l’Université Claude Bernard Lyon 1 Ecole Doctorale N° 341 Evolution Ecosystèmes Microbiologie Modélisation Spécialité de doctorat : Ecologie Microbienne Discipline : Biologie N° d’ordre NNT : 2016LYSE1143 Soutenue publiquement le 12 Septembre 2016 par : Sébastien RENOUD Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : Impact sur des communautés fonctionnelles du microbiote racinaire. Devant le jury composé de : ARSENE-PLOETZE Florence, Maître de conférences, Université de Strasbourg Rapporteur SPAEPEN Stijn, Chercheur, Institut Max Planck de Cologne Rapporteur VANDENKOORNHUYSE Philippe, Professeur, Université Rennes 1 Rapporteur RICHAUME-JOLION Agnès, Professeur, Université Lyon 1 Examinatrice MOËNNE-LOCCOZ Yvan, Professeur, Université Lyon 1 Co-directeur de thèse MULLER Daniel, Maître de conférences, Université Lyon 1 Directeur de thèse UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. -
Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments
Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments Florence Wisniewski-Dye´ 1., Kirill Borziak2,3., Gurusahai Khalsa-Moyers3, Gladys Alexandre4, Leonid O. Sukharnikov2,5, Kristin Wuichet2,5, Gregory B. Hurst6, W. Hayes McDonald6¤a, Jon S. Robertson7, Vale´rie Barbe8, Alexandra Calteau9, Zoe´ Rouy9, Sophie Mangenot8, Claire Prigent-Combaret1, Philippe Normand1, Mickae¨l Boyer1¤b, Patricia Siguier10, Yves Dessaux11, Claudine Elmerich12, Guy Condemine13, Ganisan Krishnen14¤c, Ivan Kennedy14, Andrew H. Paterson7, Victor Gonza´lez15, Patrick Mavingui1, Igor B. Zhulin2,3,5,16* 1 CNRS, UMR 5557, Ecologie Microbienne, Universite´ de Lyon, Villeurbanne, France, 2 BioEnergy Science Center, University of Tennessee–Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America, 3 Genome Science and Technology Program, University of Tennessee–Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America, 4 Department of Biochemistry, Cell and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America, 5 Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America, 6 Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America, 7 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America, 8 Institut de Ge´nomique, CEA, Ge´noscope, Evry, France, 9 Laboratoire d’Analyse Bioinformatique en Ge´nomique et Me´tabolisme CNRS UMR8030, -
List of Bacterial Type Strains Available for Distribution at CRB-JD
List of bacterial type strains available for distribution at CRB-JD Species name CRB-JD code Other collections code References LMG 1266 = WR 111 = ATCC NEW (P.B.) and TCHAN (Y.T.): Azomonas macrocytogenes (ex Azomonas macrocytogenes BR 10692 12335 = CIP 103928 = DSM 721 = Baillie, Hodgkiss, and Norris 1962, 118) nom. rev. Int. J. Syst. NCAIM B.01790 = NCIMB 8700 Bacteriol., 1982, 32, 381-382. DREYFUS (B.), GARCIA (J.L.) and GILLIS (M.): Characterization of LMG 6465 = ORS 571 = ATCC Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulating Azorhizobium caulinodans BR 5410 43989 = BCRC 15787 = DSM 5975 nitrogen-fixing bacterium isolated from Sesbania rostrata. Int. J. Syst. Bacteriol., 1988, 38, 89-98. MOREIRA (F.M.S.), CRUZ (L.), FARIA (S.M.), MARSH (T.), MARTÍNEZ- LMG 9993 = SEMIA 6401 = DSM ROMERO (E.), PEDROSA (F.O.), PITARD (R.M.) and YOUNG (J.P.W.): Azorhizobium doebereinerae BR 5401 18977 Azorhizobium doebereinerae sp. Nov. Microsymbiont of Sesbania virgata (Caz.) Pers. Syst. Appl. Microbiol., 2006, 29, 197-206. LMG 3864 = ATCC 23833 = CCUG THOMPSON (J.P.) and SKERMAN (V.B.D.): Azotobacteraceae: the Azorhizophilus paspali BR 10345 53674 = CECT 4095 = DSM 2283 = taxonomy and ecology of the aerobic nitrogen-fixing bacteria. (Azotobacter paspali) NBRC 102228 Academic Press, London, 1980, 405 pp. TARRAND (J.J.), KRIEG (N.R.) and DÖBEREINER (J.): A taxonomic study of the Spirillum lipoferum group, with descriptions of a new Sp 7 = ATCC 29145 = DSM 1690 = Azospirillum brasilense BR 11001 genus, Azospirillum gen. nov. and two species, Azospirillum BCRC 12270 = LMG 13127 lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp.