Pseudomonas Helmanticensis Sp. Nov., Isolated from Forest Soil
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Tesis Doctoral 2014 Filogenia Y Evolución De Las Poblaciones Ambientales Y Clínicas De Pseudomonas Stutzeri Y Otras Especies
TESIS DOCTORAL 2014 FILOGENIA Y EVOLUCIÓN DE LAS POBLACIONES AMBIENTALES Y CLÍNICAS DE PSEUDOMONAS STUTZERI Y OTRAS ESPECIES RELACIONADAS Claudia A. Scotta Botta TESIS DOCTORAL 2014 Programa de Doctorado de Microbiología Ambiental y Biotecnología FILOGENIA Y EVOLUCIÓN DE LAS POBLACIONES AMBIENTALES Y CLÍNICAS DE PSEUDOMONAS STUTZERI Y OTRAS ESPECIES RELACIONADAS Claudia A. Scotta Botta Director/a: Jorge Lalucat Jo Director/a: Margarita Gomila Ribas Director/a: Antonio Bennasar Figueras Doctor/a por la Universitat de les Illes Balears Index Index ……………………………………………………………………………..... 5 Acknowledgments ………………………………………………………………... 7 Abstract/Resumen/Resum ……………………………………………………….. 9 Introduction ………………………………………………………………………. 15 I.1. The genus Pseudomonas ………………………………………………….. 17 I.2. The species P. stutzeri ………………………………………………......... 23 I.2.1. Definition of the species …………………………………………… 23 I.2.2. Phenotypic properties ………………………………………………. 23 I.2.3. Genomic characterization and phylogeny ………………………….. 24 I.2.4. Polyphasic identification …………………………………………… 25 I.2.5. Natural transformation ……………………………………………... 26 I.2.6. Pathogenicity and antibiotic resistance …………………………….. 26 I.3. Habitats and ecological relevance ………………………………………… 28 I.3.1. Role of mobile genetic elements …………………………………… 28 I.4. Methods for studying Pseudomonas taxonomy …………………………... 29 I.4.1. Biochemical test-based identification ……………………………… 30 I.4.2. Gas Chromatography of Cellular Fatty Acids ................................ 32 I.4.3. Matrix Assisted Laser-Desorption Ionization Time-Of-Flight -
Evaluating the Diversity and Phylogeny of Plant Growth Promoting Bacteria Associated with Wheat (Triticum Aestivum) Growing in Central Zone of India
Int.J.Curr.Microbiol.App.Sci (2014) 3(5): 432-447 ISSN: 2319-7706 Volume 3 Number 5 (2014) pp. 432-447 http://www.ijcmas.com Original Research Article Evaluating the diversity and phylogeny of plant growth promoting bacteria associated with wheat (Triticum aestivum) growing in central zone of India Priyanka Verma1,2, Ajar Nath Yadav1, Sufia Khannam Kazy2, Anil Kumar Saxena1 and Archna Suman1* 1Division of Microbiology, Indian Agricultural Research Institute, New Delhi- 110012, India 2Department of Biotechnology, National Institute of Technology, Durgapur-713209, India *Corresponding author A B S T R A C T The diversity of plant growth promoting bacteria was investigated from wheat growing in different sites in central zone of India. Epiphytic, endophytic and rhizospheric bacteria were isolated using different growth medium. Bacterial diversity was analysed through amplified ribosomal DNA restriction analysis K e y w o r d s (ARDRA) using three restriction enzymes Alu I, Hae III, and Msp I which led to the grouping of 348 isolates into 24-29 clusters at >75% similarity index. 16S Epiphytic; rRNA gene based phylogenetic analysis, revealed that 134 strains belonged to three Endophytic; phyla namely actinobacteria, firmicutes and proteobacteria with 38 distinct species of 17 genera. Bacillus and Pseudomonas were dominant in rhizosphere while Rhizospheric; Methylobacterium were in phyllosphere. Endophytic niche specific bacteria were PGPB; identified as Delftia and Micrococcus. Sampling of different sites showed variation Drought in diversity indices. In vitro plant growth promoting activities of bacteria exposed stress; more than three beneficial traits which may act independently or concurrently. Biocontrol Phosphate solubilization and siderophores production are the predominant traits exhibited by these microbes. -
Étude Des Communautés Microbiennes Rhizosphériques De Ligneux Indigènes De Sols Anthropogéniques, Issus D’Effluents Industriels Cyril Zappelini
Étude des communautés microbiennes rhizosphériques de ligneux indigènes de sols anthropogéniques, issus d’effluents industriels Cyril Zappelini To cite this version: Cyril Zappelini. Étude des communautés microbiennes rhizosphériques de ligneux indigènes de sols anthropogéniques, issus d’effluents industriels. Sciences agricoles. Université Bourgogne Franche- Comté, 2018. Français. NNT : 2018UBFCD057. tel-01902775 HAL Id: tel-01902775 https://tel.archives-ouvertes.fr/tel-01902775 Submitted on 23 Oct 2018 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. UNIVERSITÉ DE BOURGOGNE FRANCHE-COMTÉ École doctorale Environnement-Santé Laboratoire Chrono-Environnement (UMR UFC/CNRS 6249) THÈSE Présentée en vue de l’obtention du titre de Docteur de l’Université Bourgogne Franche-Comté Spécialité « Sciences de la Vie et de l’Environnement » ÉTUDE DES COMMUNAUTES MICROBIENNES RHIZOSPHERIQUES DE LIGNEUX INDIGENES DE SOLS ANTHROPOGENIQUES, ISSUS D’EFFLUENTS INDUSTRIELS Présentée et soutenue publiquement par Cyril ZAPPELINI Le 3 juillet 2018, devant le jury composé de : Membres du jury : Vera SLAVEYKOVA (Professeure, Univ. de Genève) Rapporteure Bertrand AIGLE (Professeur, Univ. de Lorraine) Rapporteur & président du jury Céline ROOSE-AMSALEG (IGR, Univ. de Rennes) Examinatrice Karine JEZEQUEL (Maître de conférences, Univ. de Haute Alsace) Examinatrice Nicolas CAPELLI (Maître de conférences HDR, UBFC) Encadrant Christophe GUYEUX (Professeur, UBFC) Co-directeur de thèse Michel CHALOT (Professeur, UBFC) Directeur de thèse « En vérité, le chemin importe peu, la volonté d'arriver suffit à tout. -
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Biologia 66/2: 288—293, 2011 Section Cellular and Molecular Biology DOI: 10.2478/s11756-011-0021-6 The first investigation of the diversity of bacteria associated with Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) Hacer Muratoglu, Zihni Demirbag &KazimSezen* Karadeniz Technical University, Faculty of Arts and Sciences, Department of Biology, 61080 Trabzon, Turkey; e-mail: [email protected] Abstract: Colorado potato beetle, Leptinotarsa decemlineata (Say), is a devastating pest of potatoes in North America and Europe. L. decemlineata has developed resistance to insecticides used for its control. In this study, in order to find a more effective potential biological control agent against L. decemlineata, we investigated its microbiota and tested their insecticidal effects. According to morphological, physiological and biochemical tests as well as 16S rDNA sequences, microbiota was identified as Leclercia adecarboxylata (Ld1), Acinetobacter sp. (Ld2), Acinetobacter sp. (Ld3), Pseudomonas putida (Ld4), Acinetobacter sp. (Ld5) and Acinetobacter haemolyticus (Ld6). The insecticidal activities of isolates at 1.8×109 bacteria/mL dose within five days were 100%, 100%, 35%, 100%, 47% and 100%, respectively, against the L. decemlineata larvae. The results indicate that Leclercia adecarboxylata (Ld1) and Pseudomonas putida (Ld4) isolates may be valuable potential biological control agents for biological control of L. decemlineata. Key words: Leptinotarsa decemlineata; 16S rDNA; microbiota; insecticidal activity; microbial control. Abbreviations: ANOVA, one-way analysis of variance; LSD, least significant difference; PBS, phosphate buffer solution. Introduction used because of marketing concerns and limited num- ber of transgenic varieties available. Also, recombinant Potato is an important crop with ∼4.3 million tons defence molecules in plants may affect parasitoids or of production on 192,000 hectares of growing area predators indirectly (Bouchard et al. -
Comparative Analysis of the Core Proteomes Among The
Diversity 2020, 12, 289 1 of 25 Article Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species‐Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis Marios Nikolaidis 1, Dimitris Mossialos 2, Stephen G. Oliver 3 and Grigorios D. Amoutzias 1,* 1 Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 2 Microbial Biotechnology‐Molecular Bacteriology‐Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 3 Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; [email protected] * Correspondence: [email protected]; Tel.: +30‐2410‐565289; Fax: +30‐2410‐565290 Received: 22 June 2020; Accepted: 22 July 2020; Published: 24 July 2020 Abstract: The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core‐orthologues. The subsequent phylogenomic analysis revealed two well‐defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus‐level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group‐specific core proteins were also identified, with P. -
Diverse Environmental Pseudomonas Encode Unique Secondary Metabolites That Inhibit Human Pathogens
DIVERSE ENVIRONMENTAL PSEUDOMONAS ENCODE UNIQUE SECONDARY METABOLITES THAT INHIBIT HUMAN PATHOGENS Elizabeth Davis A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2017 Committee: Hans Wildschutte, Advisor Ray Larsen Jill Zeilstra-Ryalls © 2017 Elizabeth Davis All Rights Reserved iii ABSTRACT Hans Wildschutte, Advisor Antibiotic resistance has become a crisis of global proportions. People all over the world are dying from multidrug resistant infections, and it is predicted that bacterial infections will once again become the leading cause of death. One human opportunistic pathogen of great concern is Pseudomonas aeruginosa. P. aeruginosa is the most abundant pathogen in cystic fibrosis (CF) patients’ lungs over time and is resistant to most currently used antibiotics. Chronic infection of the CF lung is the main cause of morbidity and mortality in CF patients. With the rise of multidrug resistant bacteria and lack of novel antibiotics, treatment for CF patients will become more problematic. Escalating the problem is a lack of research from pharmaceutical companies due to low profitability, resulting in a large void in the discovery and development of antibiotics. Thus, research labs within academia have played an important role in the discovery of novel compounds. Environmental bacteria are known to naturally produce secondary metabolites, some of which outcompete surrounding bacteria for resources. We hypothesized that environmental Pseudomonas from diverse soil and water habitats produce secondary metabolites capable of inhibiting the growth of CF derived P. aeruginosa. To address this hypothesis, we used a population based study in tandem with transposon mutagenesis and bioinformatics to identify eight biosynthetic gene clusters (BGCs) from four different environmental Pseudomonas strains, S4G9, LE6C9, LE5C2 and S3E10. -
4.2. Biodegradation of Soil Pollutants by Microorganisms
UNIVERSITY OF PANNONIA GEORGIKON FACULTY FESTETICS DOCTORAL SCHOOL School leader: Dr. habil. Angéla Anda, DSc THE BASICS OF RESEARCH IN MICROBIOLOGICAL SOIL REMEDIATION PRACTICES DOCTORAL (PHD) THESIS Written by: Nikoletta Horváth Thesis supervisors: Dr. Borbála Biró, DSc Dr. Péter Budai, PhD 2017 KESZTHELY HUNGARY CONTENTS 1. ABSTRACTS............................................................................................................................................... 1 1.1. Abstract (English) ................................................................................................................................. 1 1.2. Kivonat (Hungarian) ............................................................................................................................. 2 1.3. Abstract (German) ................................................................................................................................ 3 2. INTRODUCTION AND IMPORTANCE OF THE TOPIC ................................................................... 4 2.1. Research background ............................................................................................................................ 4 2.2. Basis of the research ............................................................................................................................. 4 3. OBJECTIVES ............................................................................................................................................. 6 4. LITERATURE REVIEW.......................................................................................................................... -
(12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider Et Al
USOO7476532B2 (12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider et al. (45) Date of Patent: Jan. 13, 2009 (54) MANNITOL INDUCED PROMOTER Makrides, S.C., "Strategies for achieving high-level expression of SYSTEMIS IN BACTERAL, HOST CELLS genes in Escherichia coli,” Microbiol. Rev. 60(3):512-538 (Sep. 1996). (75) Inventors: J. Carrie Schneider, San Diego, CA Sánchez-Romero, J., and De Lorenzo, V., "Genetic engineering of nonpathogenic Pseudomonas strains as biocatalysts for industrial (US); Bettina Rosner, San Diego, CA and environmental process.” in Manual of Industrial Microbiology (US) and Biotechnology, Demain, A, and Davies, J., eds. (ASM Press, Washington, D.C., 1999), pp. 460-474. (73) Assignee: Dow Global Technologies Inc., Schneider J.C., et al., “Auxotrophic markers pyrF and proC can Midland, MI (US) replace antibiotic markers on protein production plasmids in high cell-density Pseudomonas fluorescens fermentation.” Biotechnol. (*) Notice: Subject to any disclaimer, the term of this Prog., 21(2):343-8 (Mar.-Apr. 2005). patent is extended or adjusted under 35 Schweizer, H.P.. "Vectors to express foreign genes and techniques to U.S.C. 154(b) by 0 days. monitor gene expression in Pseudomonads. Curr: Opin. Biotechnol., 12(5):439-445 (Oct. 2001). (21) Appl. No.: 11/447,553 Slater, R., and Williams, R. “The expression of foreign DNA in bacteria.” in Molecular Biology and Biotechnology, Walker, J., and (22) Filed: Jun. 6, 2006 Rapley, R., eds. (The Royal Society of Chemistry, Cambridge, UK, 2000), pp. 125-154. (65) Prior Publication Data Stevens, R.C., “Design of high-throughput methods of protein pro duction for structural biology.” Structure, 8(9):R177-R185 (Sep. -
Isolation of Rhizobacteria in Southwestern Québec, Canada: An
Isolation of rhizobacteria in Southwestern Québec, Canada: An investigation of their impact on the growth and salinity stress alleviation in Arabidopsis thaliana and crop plants Di Fan Department of Plant Science Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec H9X 3V9 December 2017 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of DOCTOR OF PHILOSOPHY © Di Fan, Canada, 2017 Table of contents Abstract ................................................................................................. x Résumé ................................................................................................ xiii Acknowledegments ............................................................................. xv Preface ................................................................................................ xviii Contribution of authors ................................................................................ xviii Chapter 1................................................................................................. 1 Introduction ............................................................................................ 1 Chapter 2................................................................................................. 5 Literature Review ................................................................................... 5 2.1 What are root exudates? ......................................................................... -
The Origin and Control of Microorganisms Associated With
Origin and Detection of Bacterial Species Associated with Lettuce and Salad Vegetables by Peter James Ng B Sc. (Hons) Food Science and Technology (The University of New South Wales, Australia) A thesis submitted for the degree of Doctor of Philosophy in Food Science and Technology School of Chemical Sciences and Engineering The University of New South Wales 2007 ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date …………………………………………….............. COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. -
Development of a Gut Microbiota Diagnostic Tool for Pediatric Inflammatory Bowel Disease Based on GA-Maptm Technology Platform
Development of a gut microbiota diagnostic tool for pediatric inflammatory bowel disease based on GA-mapTM technology platform DINA LILLESETH VANGEN Norwegian University of Life Science Department of Chemistry, Biotechnology and Food Science Master Thesis 2011/2012 ! ""! ! ABSTRACT Inflammatory bowel disease (IBD) is an idiopathic, severe disease, which is characterized by chronic inflammation of the gastrointestinal tract. The incidence of IBD has increased through the last decades and specially among the pediatric population. The time from onset of symptoms to a final diagnose is made, is often related to delays and for many patients it is an emotionally demanding process. Early investigation in suspected cases may reduce the delay so that a treatment can begin as soon as possible. The involvement of intestinal microflora for pathogenesis of IBD is a link to further investigations to understand the disease, and to help people who suffer from IBD. The aim of the present work was to distinguish between pediatric IBD and non-IBD by identifying signatures in the microbiota. This was accomplished by use of a diagnostic tool based on GA-mapTM technology and the use of single nucleotide primer extension (SNuPE) probes to search for complementary bacterial 16S rRNA gene sequences. Seventy-four feces samples were collected from cohort and tested against 77 SNuPE probes. Statistical analysis was performed with Partial Least Squares – Discriminant Analysis and presented specificity by 82 % and sensitivity by 86 %. Classification error presented 16 % and indicated how many that was misclassified by the model. Inflammatory bowel disease is considered to include two major disorders where Crohn’s disease is one of them, and best correlation was found between Crohn’s disease and non-IBD through statistical analysis. -
Antibiotic Resistant Pseudomonas Spp. Spoilers in Fresh Dairy Products: an Underestimated Risk and the Control Strategies
foods Review Antibiotic Resistant Pseudomonas Spp. Spoilers in Fresh Dairy Products: An Underestimated Risk and the Control Strategies Laura Quintieri , Francesca Fanelli * and Leonardo Caputo Institute of Sciences of Food Production, National Research Council of Italy, Via G. Amendola 122/O, 70126 Bari, Italy * Correspondence: [email protected]; Tel.: +39-0805929317 Received: 19 July 2019; Accepted: 23 August 2019; Published: 1 September 2019 Abstract: Microbial multidrug resistance (MDR) is a growing threat to public health mostly because it makes the fight against microorganisms that cause lethal infections ever less effective. Thus, the surveillance on MDR microorganisms has recently been strengthened, taking into account the control of antibiotic abuse as well as the mechanisms underlying the transfer of antibiotic genes (ARGs) among microbiota naturally occurring in the environment. Indeed, ARGs are not only confined to pathogenic bacteria, whose diffusion in the clinical field has aroused serious concerns, but are widespread in saprophytic bacterial communities such as those dominating the food industry. In particular, fresh dairy products can be considered a reservoir of Pseudomonas spp. resistome, potentially transmittable to consumers. Milk and fresh dairy cheeses products represent one of a few “hubs” where commensal or opportunistic pseudomonads frequently cohabit together with food microbiota and hazard pathogens even across their manufacturing processes. Pseudomonas spp., widely studied for food spoilage effects, are instead underestimated for their possible impact on human health. Recent evidences have highlighted that non-pathogenic pseudomonads strains (P. fluorescens, P. putida) are associated with some human diseases, but are still poorly considered in comparison to the pathogen P. aeruginosa.