For Peer Review
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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 -
Relevance of Phenotypic Information for the Taxonomy of Not-Yet-Cultured Microorganisms
Systematic and Applied Microbiology 42 (2019) 22–29 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms a,b,c,∗ a a,b a a Jörg Overmann , Sixing Huang , Ulrich Nübel , Richard L. Hahnke , Brian J. Tindall a Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany b Deutsches Zentrum für Infektionsforschung (DZIF), Standort Braunschweig-Hannover, Braunschweig, Germany c German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany a r t i c l e i n f o a b s t r a c t Keywords: To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and Not-yet-cultured microorganisms their names validly published. Aside from these quantitative limitations, our understanding of phenotypic Taxonomy and functional diversity of prokaryotes is also highly biased as not a single species has been described Nomenclature for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology Candidatus and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal International Code of Nomenclature of Prokaryotes genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. -
Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
Is It Essential to Sequence the Entire 16S Rrna Gene for Bacterial
» INSTRUMENTATION » Is it Essential to Sequence Introduction Bacterial Identification in the biopharmaceutical industry, especially in the Entire 16S rRNA Gene manufacturing facilities, is very important because an occurrence of a problematic microorganism in the final product could be harmful for the end user and detrimental to a company’s finances and reputation. for Bacterial Identification? Environmental Monitoring (EM) programs are the cornerstone of understanding the microbial ecology in a manufacturing facility and have become a regulatory requirement for most manufacturers. The EM program is a biological surveillance system which enables companies to quickly identify organisms which are transient or resident in their facilities before these organisms have an opportunity to contaminate a product. A properly executed EM program provides an early warning of potential contamination problems due to Sunhee Hong, PhD and equipment failure, inadequate cleaning, or deficiencies in staff hygiene Christine E. Farrance, PhD training, for example, so that problems can be corrected to prevent Charles River adulteration of the end product. The Food and Drug Administration (FDA) has published guidelines for the production of sterile drugs by aseptic processing which includes a section on EM programs, and the USP general information chapter “Microbiological Control and Monitoring of Aseptic Processing Environments” also contains detailed information regarding EM programs1. The EM program is only effective if the organisms recovered from the facility are accurately identified, so the information gathered can be used to understand the microbial control through tracking and trending and dictate appropriate remediation activities. There are several different options available for bacterial identification; however, the use of 16S rRNA gene sequences has been considered the most powerful and accurate tool, while conventional phenotypic methods often show major weaknesses2-5. -
CHAPTER 1: General Introduction and Aims 1.1 the Genus Cronobacter: an Introduction
Diversity and virulence of the genus Cronobacter revealed by multilocus sequence typing (MLST) and comparative genomic analysis Susan Manju Joseph A thesis submitted in partial fulfilment of the requirements of Nottingham Trent University for the degree of Doctor of Philosophy July 2013 Experimental work contained in this thesis is original research carried out by the author, unless otherwise stated, in the School of Science and Technology at the Nottingham Trent University. No material contained herein has been submitted for any other degree, or at any other institution. This work is the intellectual property of the author. You may copy up to 5% of this work for private study, or personal, non-commercial research. Any re-use of the information contained within this document should be fully referenced, quoting the author, title, university, degree level and pagination. Queries or requests for any other use, or if a more substantial copy is required, should be directed in the owner(s) of the Intellectual Property Rights. Susan Manju Joseph ACKNOWLEDGEMENTS I would like to express my immense gratitude to my supervisor Prof. Stephen Forsythe for having offered me the opportunity to work on this very exciting project and for having been a motivating and inspiring mentor as well as friend through every stage of this PhD. His constant encouragement and availability for frequent meetings have played a very key role in the progress of this research project. I would also like to thank my co-supervisors, Dr. Alan McNally and Prof. Graham Ball for all the useful advice, guidance and participation they provided during the course of this PhD study. -
Characterization of Arsenite-Oxidizing Bacteria Isolated from Arsenic-Rich Sediments, Atacama Desert, Chile
microorganisms Article Characterization of Arsenite-Oxidizing Bacteria Isolated from Arsenic-Rich Sediments, Atacama Desert, Chile Constanza Herrera 1, Ruben Moraga 2,*, Brian Bustamante 1, Claudia Vilo 1, Paulina Aguayo 1,3,4, Cristian Valenzuela 1, Carlos T. Smith 1 , Jorge Yáñez 5, Victor Guzmán-Fierro 6, Marlene Roeckel 6 and Víctor L. Campos 1,* 1 Laboratory of Environmental Microbiology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepcion, Concepcion 4070386, Chile; [email protected] (C.H.); [email protected] (B.B.); [email protected] (C.V.); [email protected] (P.A.); [email protected] (C.V.); [email protected] (C.T.S.) 2 Microbiology Laboratory, Faculty of Renewable Natural Resources, Arturo Prat University, Iquique 1100000, Chile 3 Faculty of Environmental Sciences, EULA-Chile, Universidad de Concepcion, Concepcion 4070386, Chile 4 Institute of Natural Resources, Faculty of Veterinary Medicine and Agronomy, Universidad de Las Américas, Sede Concepcion, Campus El Boldal, Av. Alessandri N◦1160, Concepcion 4090940, Chile 5 Faculty of Chemical Sciences, Department of Analytical and Inorganic Chemistry, University of Concepción, Concepción 4070386, Chile; [email protected] 6 Department of Chemical Engineering, Faculty of Engineering, University of Concepción, Concepcion 4070386, Chile; victorguzmanfi[email protected] (V.G.-F.); [email protected] (M.R.) * Correspondence: [email protected] (R.M.); [email protected] (V.L.C.) Abstract: Arsenic (As), a semimetal toxic for humans, is commonly associated -
Fictibacillus Phosphorivorans Gen. Nov., Sp. Nov. and Proposal to Reclassify
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 2934–2944 DOI 10.1099/ijs.0.049171-0 Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus Stefanie P. Glaeser,1 Wolfgang Dott,2 Hans-Ju¨rgen Busse3 and Peter Ka¨mpfer1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, Germany Peter Ka¨mpfer 2Institut fu¨r Hygiene und Umweltmedizin, RWTH Aachen, Germany peter.kaempfer 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, @umwelt.uni-giessen.de Austria A Gram-positive-staining, aerobic, endospore-forming bacterium (Ca7T) was isolated from a bioreactor showing extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strain Ca7T was grouped in the genus Bacillus, most closely related to Bacillus nanhaiensis JSM 082006T (100 %), Bacillus barbaricus V2-BIII-A2T (99.2 %) and Bacillus arsenicus Con a/3T (97.7 %). Moderate 16S rRNA gene sequence similarities were found to the type strains of the species Bacillus gelatini and Bacillus rigui (96.4 %), Bacillus macauensis (95.1 %) and Bacillus solisalsi (96.1 %). All these species were grouped into a monophyletic cluster and showed very low sequence similarities (,94 %) to the type species of the genus Bacillus, Bacillus subtilis.Thequinonesystemof strain Ca7T consists predominantly of menaquinone MK-7. The polar lipid profile exhibited the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, minor compounds of an unidentified phospholipid and an aminophospholipid were detected. No glycolipids were found in strain Ca7T, which was consistent with the lipid profiles of B. -
Hyphal Proteobacteria, Hirschia Baltica Gen. Nov. , Sp. Nov
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1990, p. 443451 Vol. 40. No. 4 0020-7713/9O/040443-O9$02.00/0 Copyright 0 1990, International Union of Microbiological Societies Taxonomic and Phylogenetic Studies on a New Taxon of Budding, Hyphal Proteobacteria, Hirschia baltica gen. nov. , sp. nov. HEINZ SCHLESNER," CHRISTINA BARTELS, MANUEL SITTIG, MATTHIAS DORSCH, AND ERKO STACKEBRANDTT Institut fur Allgemeine Mikrobiologie, Christian-Albrecht-Universitat, 2300 Kiel, Federal Republic of Germany Four strains of budding, hyphal bacteria, which had very similar chemotaxonomic properties, were isolated from the Baltic Sea. The results of DNA-DNA hybridization experiments, indicated that three of the new isolates were closely related, while the fourth was only moderately related to the other three. Sequence signature and higher-order structural detail analyses of the 16s rRNA of strain IFAM 141gT (T = type strain) indicated that this isolate is related to the alpha subclass of the class Proteobacteriu. Although our isolates resemble members of the genera Hyphomicrobium and Hyphomonas in morphology, assignment to either of these genera was excluded on the basis of their markedly lower DNA guanine-plus-cytosine contents. We propose that these organisms should be placed in a new genus, Hirschiu baltica is the type species of this genus, and the type strain of H. bdtica is strain IFAM 1418 (= DSM 5838). Since the first description of a hyphal, budding bacterium, no1 and formamide were tested at concentrations of 0.02 and Hyphomicrobium vulgare (53), only the following additional 0.1% (vol/vol). Utilization of nitrogen sources was tested in genera having this morphological type have been formally M9 medium containing glucose as the carbon source. -
Sphingopyxis Italica, Sp. Nov., Isolated from Roman Catacombs 1 2
View metadata, citation and similar papers at core.ac.uk brought to you by CORE IJSEM Papers in Press. Published December 21, 2012 as doi:10.1099/ijs.0.046573-0 provided by Digital.CSIC 1 Sphingopyxis italica, sp. nov., isolated from Roman catacombs 2 3 Cynthia Alias-Villegasª, Valme Jurado*ª, Leonila Laiz, Cesareo Saiz-Jimenez 4 5 Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, 6 Apartado 1052, 41080 Sevilla, Spain 7 8 * Corresponding author: 9 Valme Jurado 10 Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC 11 Apartado 1052, 41080 Sevilla, Spain 12 Tel. +34 95 462 4711, Fax +34 95 462 4002 13 E-mail: [email protected] 14 15 ª These authors contributed equally to this work. 16 17 Keywords: Sphingopyxis italica, Roman catacombs, rRNA, sequence 18 19 The sequence of the 16S rRNA gene from strain SC13E-S71T can be accessed 20 at Genbank, accession number HE648058. 21 22 A Gram-negative, aerobic, motile, rod-shaped bacterium, strain SC13E- 23 S71T, was isolated from tuff, the volcanic rock where was excavated the 24 Roman Catacombs of Saint Callixtus in Rome, Italy. Analysis of 16S 25 rRNA gene sequences revealed that strain SC13E-S71T belongs to the 26 genus Sphingopyxis, and that it shows the greatest sequence similarity 27 with Sphingopyxis chilensis DSMZ 14889T (98.72%), Sphingopyxis 28 taejonensis DSMZ 15583T (98.65%), Sphingopyxis ginsengisoli LMG 29 23390T (98.16%), Sphingopyxis panaciterrae KCTC12580T (98.09%), 30 Sphingopyxis alaskensis DSM 13593T (98.09%), Sphingopyxis 31 witflariensis DSM 14551T (98.09%), Sphingopyxis bauzanensis DSM 32 22271T (98.02%), Sphingopyxis granuli KCTC12209T (97.73%), 33 Sphingopyxis macrogoltabida KACC 10927T (97.49%), Sphingopyxis 34 ummariensis DSM 24316T (97.37%) and Sphingopyxis panaciterrulae T 35 KCTC 22112 (97.09%). -
Biodiversité Microbienne Dans Les Milieux Extrêmes Salés Du Nord-Est Algérien
اﻟﺟﻣﮭورﯾﺔ اﻟﺟزاﺋرﯾﺔ اﻟدﯾﻣﻘراطﯾﺔ اﻟﺷﻌﺑﯾﺔ République Algérienne Démocratique et Populaire وزارة اﻟتــﻋﻠﯾم اﻟﻊــــاﻟﻲ و اﻟبـــﺣث اﻟﻊـــﻟﻣﻲ Ministère de l’Enseignement Supérieur et de la Recherche Scientifique جـــاﻣﻌﺔ ﺑـﺎﺗـﻧـــــــــــــــﺔ Université Mustapha Ben Boulaid- Batna 2 2 كــــﻟﯾــــــﺔ عـــــﻟوم اﻟطــﺑﯾﻌـــــــﺔ ـوالحــــﯾﺎة Faculté des Sciences de la Nature et de la Vie ﻗـــﺳم اﻟﻣﯾﻛروﺑﯾوﻟوﺟﯾـــــــﺎ و اﻟﺑﯾوﻛﯾﻣﯾـــــــﺎء Département de Microbiologie et Biochimie Réf : …………………………… اﻟﻣـرﺟﻊ :………………….…… Thèse présentée par Taha MENASRIA En vue de l’obtention du diplôme de Doctorat en ScienceS Filière : Sciences Biologiques Spécialité : Microbiologie Appliquée Thème Biodiversité microbienne dans les milieux extrêmes salés du Nord-Est Algérien Devant le jury composé de : Président : Dr. Kamel AISSAT (Professeur) Univ. de Batna 2 Directeur de thèse : Dr. Hocine HACÈNE (Professeur) Univ. d’Alger (USTHB) Co-directeur de thèse : Dr. Abdelkrim SI BACHIR (Professeur) Univ. de Batna 2 Examinateur : Dr. Yacine BENHIZIA (Professeur) Univ. de Constantine 1 Examinateur : Dr. Mahmoud KITOUNI (Professeur) Univ. de Constantine 1 Examinateur : Dr. Lotfi LOUCIF (Maître de conférences ‘A’) Univ. de Batna 2 Membre invité : Dr. Ammar AYACHI (Professeur) Univ. de Batna 1 Année universitaire : 2019-2020 Remerciements C’est un devoir d’exprimer mes remerciements et reconnaissances à travers cette thèse à tous ceux qui par leurs aides, encouragements et leurs conseils ont facilité, de près ou de loin, à l’élaboration et à la réalisation de ce modeste travail. Mes remerciements vont en premier ordre et particulièrement à : Dr. Hocine HACÈNE (Professeur à l’Université d’USTHB, Alger) pour le grand honneur qu’il m’a fait en acceptant de diriger ce travail, pour ses conseils et ses encouragements durant la réalisation de cette thèse. -
BIODATA 1) Name : Dr. Ch. Sasikala 2) Designation
BIODATA 1) Name : Dr. Ch. Sasikala 2) Designation : Professor and Chairperson, Board of Studies in Environemntal Science and Technology 3) Address a) Official : Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad – 500 085 INDIA Phone: 040-23158661 /2/3/4 Extn.3480 Email: [email protected] [email protected] , [email protected] b) Home : 5-3-357, Rashtrapathi Road, Secunderabad 500 003 INDIA Phone: Res. 040-27535462 (R) Mobile : 9000796341 4) Date of Birth : 9 th March 1963 5) Nature of work : Teaching/Research 6) Research experience : 30 years of research experience Including 26 years of post-doctoral experience 7) PG teaching experience : 21 years 8) Field of specialization : Environmental microbiology and biotechnology (Bacterial diversity, Bioprospecting, biodegradation and Bioremediation) 9) Research publications : 191 (Annexure A) (In standard refereed journals) Cumulative impact factor: 440 h index: 28; Number of citations: ~3,000 1 10) Academic qualifications and career record: a) Degrees : B.Sc., B.Ed., M.Sc., Ph.D. b) Details of Educational qualifications : Exam Subjects Board/ Year of Class/ % of passed University passing Division Marks S.S.C Tel. Hindi, Board of 1978 I 70 Eng. Maths, Secondary Ed. Gen. Sci. and Andhra Social studies Pradesh Intermediate Biol. Phy. Board of 1980 I 76.5 Chem. Intermediate Education, A.P B.Sc. Bot. Chem. Osmania 1983 I 83.2 Microbiol University B.Ed. Life Sciences Osmania 1984 I 68 University M.Sc. Applied Bharathiar 1986 I 70 Microbiology University (university second -
Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fenᰔ† Alexandra Hamberger,1 Marcus A
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, May 2008, p. 3112–3120 Vol. 74, No. 10 0099-2240/08/$08.00ϩ0 doi:10.1128/AEM.00193-08 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fenᰔ† Alexandra Hamberger,1 Marcus A. Horn,1* Marc G. Dumont,2 J. Colin Murrell,2 and Harold L. Drake1 Department of Ecological Microbiology, University of Bayreuth, 95445 Bayreuth, Germany,1 and Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom2 Received 22 January 2008/Accepted 20 March 2008 16S rRNA-based stable isotope probing identified active xylose- and glucose-fermenting Bacteria and active Archaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH4- emitting fen. Xylose and glucose were converted to fatty acids, CO2,H2, and CH4 under moderately acidic, anoxic conditions, indicating that the fen harbors moderately acid-tolerant xylose- and glucose-using fermen- ters, as well as moderately acid-tolerant methanogens. Organisms of the families Acidaminococcaceae, Aero- monadaceae, Clostridiaceae, Enterobacteriaceae, and Pseudomonadaceae and the order Actinomycetales, including hitherto unknown organisms, utilized xylose- or glucose-derived carbon, suggesting that highly diverse facul- tative aerobes and obligate anaerobes contribute to the flow of carbon in the fen under anoxic conditions. Uncultured Euryarchaeota (i.e., Methanosarcinaceae and Methanobacteriaceae) and Crenarchaeota species were