DOCSLIB.ORG

A Comparative Genomics Study of the Genes Involved in the Catabolic Pathways of Naphthalene”

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Comparative Genomics Study of the Genes Involved in the Catabolic Pathways of Naphthalene” Título del Trabajo Final “Bacterial degradation of petroleum hydrocarbons; a comparative genomics study of the genes involved in the catabolic pathways of naphthalene” Nombre Estudiante: Athanasía Varsaki Plan de Estudios del Estudiante: Bioinformática Área del trabajo final: Microbiología, biotecnología y biología molecular Nombre Consultor/a: Paloma Pizarro Tobías Nombre Profesor/a responsable de la asignatura: Paloma Pizarro Tobías Fecha Entrega: 02/01/2018 Esta obra está sujeta a una licencia de Reconocimiento-NoComercial- SinObraDerivada 3.0 España de Creative Commons Licencias alternativas (elegir alguna de las siguientes y sustituir la de la página anterior) A) Creative Commons: Esta obra está sujeta a una licencia de Reconocimiento-NoComercial- SinObraDerivada 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-NoComercial-CompartirIgual 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-NoComercial 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-SinObraDerivada 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento-CompartirIgual 3.0 España de Creative Commons Esta obra está sujeta a una licencia de Reconocimiento 3.0 España de Creative Commons B) GNU Free Documentation License (GNU FDL) Copyright © AÑO TU-NOMBRE. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back- Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License". C) Copyright © (el autor/a) Reservados todos los derechos. Está prohibido la reproducción total o parcial de esta obra por cualquier medio o procedimiento, comprendidos la impresión, la reprografía, el microfilme, el tratamiento informático o cualquier otro sistema, así como la distribución de ejemplares mediante alquiler y préstamo, sin la autorización escrita del autor o de los límites que autorice la Ley de Propiedad Intelectual. FICHA DEL TRABAJO FINAL Bacterial degradation of petroleum hydrocarbons; a comparative genomics Título del trabajo: study of the genes involved in the catabolic pathways of naphthalene Nombre del autor: Athanasia Varsaki Nombre del consultor/a: Paloma Pizarro Tobías Nombre del PRA: Paloma Pizarro Tobías Fecha de entrega (mm/aaaa): 01/2018 Titulación:: Bioinformática Microbiología, biotecnología y biología Área del Trabajo Final: molecular Idioma del trabajo: Ingles Bioremediation; biodegradation; catabolic Palabras clave genes Resumen del Trabajo (máximo 250 palabras): Los compuestos aromáticos se encuentran entre los contaminantes más prevalentes y persistentes en el medio ambiente. El suelo y los sedimentos contaminados con petróleo suelen contener una mezcla de hidrocarburos aromáticos policíclicos (PAHs) y heterocíclicos. La información sobre el catabolismo de compuestos aromáticos xenobióticos naturales por bacterias ha aumentado considerablemente en los ultimos años. Los estudios detallados más recientes incluyen en general pocas rutas metabólicas, en un rango relativamente limitado de bacterias, en su mayoría del género Pseudomonas, y no hay estudios disponibles con respecto a la genómica comparativa de estas i bacterias. En este trabajo proponemos un estudio genético comparativo de los genes involucrados en la ruta catabólica del naftaleno. Usando la enzima naftaleno 1,2-dioxigenasa ferrodoxin-NAD(P)+ reductasa (NahAa, Acc. Number: AAS79488.1) de Pseudomonas putida como marcador filogenético, intentamos identificar las proteínas homólogas presentes en las bases de datos de NCBI. Por genómica comparativa, pretendemos identificar los posibles grupos de las vías catabólicas del naftaleno y la estructura de los operones. Los resultados de este estudio indican que las bacterias degradan naftaleno principalmente a través de la vía "clásica" de naftaleno, descrita para el género Pseudomonas o a través de la ruta alternativa del gentisato-salicilato. Abstract (in English, 250 words or less): Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. In recent years there has been a quantum leap in the information published about the catabolism of natural xenobiotic aromatic compounds by bacteria. At present the most detailed studies have been carried out on relatively few metabolic pathways, in a rather limited range of bacteria, mostly of the genus Pseudomonas, but there is no study available regarding the comparative genomics of these bacteria. Here we propose a comparative genetics study of the genes involved in the catabolic pathway of naphthalene, using the naphthalene 1,2-dioxygenase system ferredoxin-NAD(P)+ reductase enzyme (NahAa, Acc. Number: AAS79488.1) from Pseudomonas putida as a phylogenetic marker. By that way we intent to identify the homologous proteins present in the NCBI databases and through the proteins make conclusions about possible groups of the catabolic pathways of naphthalene and their operon structure. Results of this study indicate that bacteria mainly degrade naphthalene through either the “classic” nah pathway described for Pseudomonas genus or the alternative gentisate-salicylate pathway. ii Index 1. Introducción .................................................................................................... 1 1.1 Contexto y justificación del Trabajo ........................................................... 1 1.2 Objetivos del Trabajo ................................................................................. 4 1.3 Enfoque y método seguido ........................................................................ 4 1.4 Planificación del Trabajo ........................................................................... 7 1.5 Breve sumario de los productos obtenidos ................................................ 8 1.6 Breve descripción de los otros capítulos de la memoria............................ 8 2. Resultados y Discusión .................................................................................. 9 2.1 Construction of the dataset ........................................................................ 9 2.2 Construction of protein profiles, alignments and phylogenetic trees ........ 10 2.3 Localization of the genes/operons ........................................................... 17 2.3.1 Putative nah catabolising operons composed by 12 genes .................. 17 2.3.2 Putative nah catabolising operons composed by 11 genes .................. 22 2.3.3 Putative nah catabolising operons composed by 9 genes .................... 25 2.3.4 Putative nah catabolising operons composed by 7 genes .................... 28 2.3.5 Putative nah catabolising operons composed by 6 genes .................... 34 2.3.6 Putative nah catabolising operons composed by 4 genes .................... 37 2.3.7 Putative nah catabolising operons composed by 3 genes .................... 39 3. Conclusions and general discussion. ........................................................... 40 4. Glosario ........................................................................................................ 44 5. Bibliografía ................................................................................................... 45 6. Anexos ......................................................................................................... 50 iii Lista de figuras Figure 1: Proposed bacterial catabolic pathway of naphthalene Figure 2: Chronogram of this study Figure 3: Reaction catalyzed by the three-component naphthalene dioxygenase (NDO) system. Figure 4: A representative alignment (it is shown only 15 protein from the 224 used) of the proteins retrieved from the PSI-BLAST. Conserved amino acids are shown with an asterisk. Figure 5: The maximum-likelihood (ML) phylogenetic tree was built with the 224 NahAa homologues present in NCBI database un to October 2017. Bootstrap values are indicated at the corresponding nodes of the ML tree. The cut-off value for the condensed tree was chosen at bootstrap value=50%. The NahAa from P. putida SG1 is indicated with a red circle. Proteins from plasmids are indicated with a blue circle. Figure 6: Genome-to-genome comparison of the nah operon from P. putida strain BS202 with the putative operon from Polaromonas sp. JS666. Analysis was performed with EasyFig2.2.2. Figure 7: Genetic organization of the putative nah operon from Polaromonas sp. JS666. Color code: genes reported as involved in naphthalene degradation are shown in light blue color, genes reported as involved in degradation of other aromatic compounds are shown in light orange colour, genes of other metabolic pathways are shown in black. Figure 8: Proposed model for the conversion of salicylate to gentisate. Figure 9: Genome-to-genome comparison of the nah operon from P. putida strain BS202 with the putative operon from B. multivorans strain DDS 15A-1. Figure 10: Genetic organization of the putative nah operon from B. multivorans strain DDS 15A-1. Color code: light blue: genes reported as involved in naphthalene degradation; orange: genes reported as involved in other degradation routes; black: genes of other metabolic pathways. iv Figure 11: Genetic organization of the putative nah
Load more

Recommended publications
  • Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism
    fmicb-10-02556 November 4, 2019 Time: 15:40 # 1 ORIGINAL RESEARCH published: 06 November 2019 doi: 10.3389/fmicb.2019.02556 Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism Charlotte Peeters1, Evelien De Canck1, Margo Cnockaert1, Evie De Brandt1, Cindy Snauwaert2, Bart Verheyde1, Eliza Depoorter1, Theodore Spilker3, John J. LiPuma3 and Peter Vandamme1,2* 1 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium, 2 BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent Edited by: University, Ghent, Belgium, 3 Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States Iain Sutcliffe, Northumbria University, United Kingdom Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea Reviewed by: reference strains and field isolates revealed several clusters that included no taxonomic Martin W. Hahn, reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 University of Innsbruck, Austria Stephanus Nicolaas Venter, strains for whole-genome sequence analysis and for a comparative genomics study that University of Pretoria, South Africa also included 41 publicly available Pandoraea genome sequences. The phylogenomic Aharon Oren, The Hebrew University of Jerusalem, analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise Israel digital DNA–DNA hybridization values and their
    [Show full text]
  • Genomic and Proteomic Analysis of Lignin Degrading and Polyhydroxyalkanoate Accumulating Β‑Proteobacterium Pandoraea Sp
    Kumar et al. Biotechnol Biofuels (2018) 11:154 https://doi.org/10.1186/s13068-018-1148-2 Biotechnology for Biofuels RESEARCH Open Access Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β‑proteobacterium Pandoraea sp. ISTKB Madan Kumar1, Sandhya Verma2, Rajesh Kumar Gazara2, Manish Kumar1, Ashok Pandey3, Praveen Kumar Verma2* and Indu Shekhar Thakur1* Abstract Background: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysac- charide-based biorefnery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to fnd the impor- tant enzymes for polymer utilization. Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identifed various candidate genes responsible for lignin degradation and PHA production.
    [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]
  • Acidovorax Citrulli
    Bulletin OEPP/EPPO Bulletin (2016) 46 (3), 444–462 ISSN 0250-8052. DOI: 10.1111/epp.12330 European and Mediterranean Plant Protection Organization Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes PM 7/127 (1) Diagnostics Diagnostic PM 7/127 (1) Acidovorax citrulli Specific scope Specific approval and amendment This Standard describes a diagnostic protocol for Approved in 2016-09. Acidovorax citrulli.1 This Standard should be used in conjunction with PM 7/76 Use of EPPO diagnostic protocols. strain, were mainly isolated from non-watermelon, cucurbit 1. Introduction hosts such as cantaloupe melon (Cucumis melo var. Acidovorax citrulli is the causal agent of bacterial fruit cantalupensis), cucumber (Cucumis sativus), honeydew blotch and seedling blight of cucurbits (Webb & Goth, melon (Cucumis melo var. indorus), squash and pumpkin 1965; Schaad et al., 1978). This disease was sporadic until (Cucurbita pepo, Cucurbita maxima and Cucurbita the late 1980s (Wall & Santos, 1988), but recurrent epi- moschata) whereas Group II isolates were mainly recovered demics have been reported in the last 20 years (Zhang & from watermelon (Walcott et al., 2000, 2004; Burdman Rhodes, 1990; Somodi et al., 1991; Latin & Hopkins, et al., 2005). While Group I isolates were moderately 1995; Demir, 1996; Assis et al., 1999; Langston et al., aggressive on a range of cucurbit hosts, Group II isolates 1999; O’Brien & Martin, 1999; Burdman et al., 2005; Har- were highly aggressive on watermelon but moderately ighi, 2007; Holeva et al., 2010; Popovic & Ivanovic, 2015). aggressive on non-watermelon hosts (Walcott et al., 2000, The disease is particularly severe on watermelon (Citrullus 2004).
    [Show full text]
  • Quorum Sensing Activity in Pandoraea Pnomenusa RB38
    Sensors 2014, 14, 10177-10186; doi:10.3390/s140610177 OPEN ACCESS sensors ISSN 1424-8220 www.mdpi.com/journal/sensors Article Quorum Sensing Activity in Pandoraea pnomenusa RB38 Robson Ee, Yan-Lue Lim, Lin-Xin Kin, Wai-Fong Yin and Kok-Gan Chan * Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: [email protected] (R.E.); [email protected] (Y.-L.L.); [email protected] (L.-X.K.); [email protected] (W.-F.Y.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +60-37967-5162; Fax: +60-37967-4509. Received: 5 March 2014; in revised form: 25 May 2014 / Accepted: 28 May 2014 / Published: 10 June 2014 Abstract: Strain RB38 was recovered from a former dumping area in Malaysia. MALDI-TOF mass spectrometry and genomic analysis identified strain RB-38 as Pandoraea pnomenusa. Various biosensors confirmed its quorum sensing properties. High resolution triple quadrupole liquid chromatography–mass spectrometry analysis was subsequently used to characterize the N-acyl homoserine lactone production profile of P. pnomenusa strain RB38, which validated that this isolate produced N-octanoyl homoserine lactone as a quorum sensing molecule. This is the first report of the production of N-octanoyl homoserine lactone by P. pnomenusa strain RB38. Keywords: matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF); mass spectrometry (MS); cell-to cell communication; triple quodruopole liquid chromatography mass spectrometry (LC-MS/MS); N-octanoyl homoserine lactone (C8-HSL) 1. Introduction Pandoraea is a Gram-negative rod shape proteobacteria of the Burkholderiaceae family that is often isolated from sputa of cystic fibrosis patients and soil [1].
    [Show full text]
  • Genome of Ca. Pandoraea Novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas Esmeraldas
    fmicb-08-01940 September 30, 2017 Time: 16:0 # 1 ORIGINAL RESEARCH published: 04 October 2017 doi: 10.3389/fmicb.2017.01940 Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas Alexei Y. Kostygov1,2†, Anzhelika Butenko1,3†, Anna Nenarokova3,4, Daria Tashyreva3, Pavel Flegontov1,3,5, Julius Lukeš3,4 and Vyacheslav Yurchenko1,3,6* 1 Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia, 2 Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia, 3 Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceskéˇ Budejovice,ˇ Czechia, 4 Faculty of Sciences, University of South Bohemia, Ceskéˇ Budejovice,ˇ Czechia, 5 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 6 Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czechia We have sequenced, annotated, and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it Edited by: has all the hallmarks of the endosymbionts’ genomes, such as significantly reduced João Marcelo Pereira Alves, University of São Paulo, Brazil size, extensive gene loss, low GC content, numerous gene rearrangements, and Reviewed by: low codon usage bias. In addition, Ca. P. novymonadis lacks mobile elements, Zhao-Rong Lun, has a strikingly low number of pseudogenes, and almost all genes are single Sun Yat-sen University, China Vera Tai, copied. This suggests that it already passed the intensive period of host adaptation, University of Western Ontario, Canada which still can be observed in the genome of Polynucleobacter necessarius, a *Correspondence: certainly recent endosymbiont.
    [Show full text]
  • Pandoraea Apista Bacteremia in a COVID-Positive Man: a Rare Coinfection Case Report from North India
    Published online: 2021-06-28 THIEME 192 Case Pandoraea Report apistain a COVID Patient Singh et al. Pandoraea apista Bacteremia in a COVID-Positive Man: A Rare Coinfection Case Report from North India Sweta Singh1 Chinmoy Sahu1 , Sangram Singh Patel1 Atul Garg1 Ujjala Ghoshal1 1Department of Microbiology, Sanjay Gandhi Post Graduate Address for correspondence Chinmoy Sahu, MD (Microbiology) Institute of Medical Sciences, Lucknow, Uttar Pradesh, India Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh 226014, India (e-mail: [email protected]). J Lab Physicians 2021;13:192–194. Abstract Pandoraea apista is a novel gram-negative bacillus usually isolated from respiratory specimens of cystic fibrosis patients. Few cases of bacteremia have also been reported due to this rare pathogen. Emergence of multidrug-resistant isolates of this bacillus is of grave concern. Here, we report a very interesting and unusual case of Pandoraea Keywords apista bacteremia in a coronavirus disease (COVID)–positive elderly diabetic man suf- ► Pandoraea apista fering from pneumonia. Prompt isolation and antibiotic sensitivity testing guided the ► bacillus patient’s treatment and yielded favorable outcome. The need of automated methods ► cystic fibrosis for identification and sensitivity testing limits the reporting of this rare but important ► bacteremia pathogen in hospital settings. Detailed research work and studies are needed in this ► COVID direction to better understand this pathogen and its clinical manifestations for better ► pneumonia patient outcome. Introduction report a case of bacteremia caused by Pandoraea apista in a COVID-positive elderly man suffering from pneumonia. Pandoraea species is a newly emerging multidrug-resistant pathogen usually isolated from cystic fibrosis (CF) patients.
    [Show full text]
  • 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 ..............................................................................................................................
    [Show full text]
  • CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
    report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations.
    [Show full text]
  • Complete Assembly of the Genome of an Acidovorax Citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
    fmicb-10-01400 June 19, 2019 Time: 15:19 # 1 ORIGINAL RESEARCH published: 20 June 2019 doi: 10.3389/fmicb.2019.01400 Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species Rongzhi Yang1, Diego Santos Garcia2, Francisco Pérez Montaño1,3, Gustavo Mateus da Silva1, Mei Zhao4, Irene Jiménez Guerrero1, Tally Rosenberg1, Gong Chen4, Inbar Plaschkes5, Shai Morin2, Ron Walcott4 and Saul Burdman1* 1 Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel, 2 Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel, 3 Department of Microbiology, University of Seville, Seville, Spain, 4 Department of Plant Pathology, University of Georgia, Athens, GA, United States, 5 Bioinformatics Unit, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel Edited by: Martin G. Klotz, Washington State University, Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat United States to cucurbit crop production worldwide. Based on genetic and phenotypic properties, Reviewed by: A. citrulli strains are divided into two major groups: group I strains have been generally Robert Wilson Jackson, isolated from melon and other non-watermelon cucurbits, while group II strains are University of Reading, United Kingdom closely associated with watermelon. In a previous study, we reported the genome Tingchang Zhao, of the group I model strain, M6. At that time, the M6 genome was sequenced by Chinese Academy of Agricultural Sciences, China MiSeq Illumina technology, with reads assembled into 139 contigs.
    [Show full text]
  • Identification of Pseudomonas Species and Other Non-Glucose Fermenters
    UK Standards for Microbiology Investigations Identification of Pseudomonas species and other Non- Glucose Fermenters Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 17 | Issue no: 3 | Issue date: 13.04.15 | Page: 1 of 41 © Crown copyright 2015 Identification of Pseudomonas species and other Non-Glucose Fermenters Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories
    [Show full text]
  • Eukaryota Fungi Bacteria
    Streptomyces-antibioticus Streptomyces-griseus Streptomyces-lincolnensis Streptomyces-phaeochromogenes Streptomyces-scabiei Streptomyces-violaceoruber Streptomyces-viridochromogenes Streptomyces-griseoruber Streptomyces-sclerotialus Streptomyces-olivochromogenes Streptomyces-cellulosae Streptomyces-chartreusis Streptomyces-cattleya Streptomyces-galbus Streptomyces-caelestis Streptomyces-subrutilus Streptomyces-acidiscabies Streptomyces-diastatochromogenes Streptomyces-neyagawaensis Streptomyces-canus Streptomyces-yerevanensis Streptomyces-afghaniensis Streptomyces-bicolor Streptomyces-cellostaticus Streptomyces-griseorubiginosus Streptomyces-phaeopurpureus Streptomyces-prasinus Streptomyces-prunicolor Streptomyces-pseudovenezuelae Streptomyces-resistomycificus Streptomyces Streptomyces-iakyrus Streptomyces-katrae Streptomyces-mirabilis Streptomyces-peruviensis Streptomyces-regalis Streptomyces-torulosus Streptomyces-turgidiscabies Streptomyces-ipomoeae Streptomyces-phaeoluteigriseus Streptomyces-curacoi Streptomyces-azureus Streptomyces-europaeiscabiei Streptomyces-stelliscabiei Streptomyces-puniciscabiei Streptomyces-aureus Streptomyces-ossamyceticus Streptomyces-variegatus Streptomyces-roseochromogenus Streptomyces-xylophagus Streptomyces-sviceus Streptomyces-fulvoviolaceus Streptomyces-bungoensis Streptomyces-erythrochromogenes Streptomycetaceae Streptomyces-davaonensis Streptomyces-olindensis Streptomyces-rubellomurinus Streptomyces-indicus Streptomyces-caeruleatus Streptomyces-hokutonensis Streptomyces-humi Streptomyces-jeddahensis
    [Show full text]