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Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. -
Pseudomonas Pseudoalcaligenes Subsp. Citruzzi Subsp. Nov
OO20-7713/78/OO28-0 I 17$02.OO/O INTERNATIONALJOLJRNAL OF SYSTEMATIC BACTERIOLOGY,Jan. 1978, p. 117-125 Vol. 28, No. I Copyright 0 1978 International Association of Microbiological Societies Printed in U.S. A. Pseudomonas pseudoalcaligenes subsp. citruZZi subsp. nov. N. W. SCHAAD,' G. SOWELL, JR.,' R. W. GOTH,3 R. R. COLWELL? AND R. E. WEBB3 Department of Plant Pathology, University of Georgia, Athens, Georgia .30602l; and Agricultural Research Seruice, Georgia Experiment Station, Experiment, Georgia 30212; Agricultural Research Seruice, P G G I, Beltsuille, Maryland 29705'; and Department of Microbiology, University of Maryland, College Park, Maryland 20747L Ten nonfluorescent Pseudomonas strains isolated from water-soaked lesions on cotyledons of plants of five Citrullus lanatus (watermelon) plant introductions were characterized and compared phenotypically with 22 other pseudomonads. The strains were distinguished phenotypically from other known plant pathogenic pseudomonads. The watermelon bacterium was aerobic. Cells were rod-shaped, gram negative, and motile by means of a single polar flagellum. They were nonfluorescent and grew at 41°C but not at 4°C. Oxidase production and the 2- ketogluconate reaction were positive. The 10 strains utilized p-alanine, rA-leucine, D-serine, n-propanal, ethanol, ethanolamine, citrate, and fructose for growth. No growth occurred with sucrose or glucose. Their deoxyribonucleic acid base com- position was 66 1mol% guanine plus cytosine. The bacterium is phenotypically similar to P. pseudoalcaligenes but differs from it in being pathogenic to water- melon, Cucumis melo (cantaloupe), Cucumis sativus (cucumber), and Cucurbita pep0 (squash). The name P. pseudoalcaligenes subsp. citrulli is proposed for the new subspecies, of which strain C-42 (= ATCC 29625) is the type strain. -
Comparative Genomic Analysis of Three Pseudomonas
microorganisms Article Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column Ashish Pathak 1, Paul Stothard 2 and Ashvini Chauhan 1,* 1 Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA; [email protected] 2 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-850-412-5119; Fax: +1-850-561-2248 Abstract: The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because Citation: Pathak, A.; Stothard, P.; of their immense metabolic and ecological potential. To obtain a comprehensive understanding on Chauhan, A. Comparative Genomic this aspect, we previously reported on the isolation and preliminary genomic characterization of Analysis of Three Pseudomonas Species three Pseudomonas species isolated from minced oyster tissue (P. -
Pseudomonas Helmanticensis Sp. Nov., Isolated from Forest Soil
International Journal of Systematic and Evolutionary Microbiology (2014), 64, 2338–2345 DOI 10.1099/ijs.0.063560-0 Pseudomonas helmanticensis sp. nov., isolated from forest soil Martha-Helena Ramı´rez-Bahena,1,2 Maria Jose´ Cuesta,1 Jose´ David Flores-Fe´lix,3 Rebeca Mulas,4 Rau´l Rivas,2,3 Joao Castro-Pinto,5 Javier Bran˜as,5 Daniel Mulas,5 Fernando Gonza´lez-Andre´s,4 Encarna Vela´zquez2,3 and A´ lvaro Peix1,2 Correspondence 1Instituto de Recursos Naturales y Agrobiologı´a, IRNASA-CSIC, Salamanca, Spain A´ lvaro Peix 2Unidad Asociada Grupo de Interaccio´n Planta-Microorganismo, [email protected] Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain 3Departamento de Microbiologı´a y Gene´tica, Universidad de Salamanca, Salamanca, Spain 4Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de Leo´n, Leo´n, Spain 5Fertiberia S. A., Madrid, Spain A bacterial strain, OHA11T, was isolated during the course of a study of phosphate-solubilizing bacteria occurring in a forest soil from Salamanca, Spain. The 16S rRNA gene sequence of strain OHA11T shared 99.1 % similarity with respect to Pseudomonas baetica a390T, and 98.9 % similarity with the type strains of Pseudomonas jessenii, Pseudomonas moorei, Pseudomonas umsongensis, Pseudomonas mohnii and Pseudomonas koreensis. The analysis of housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation to the genus Pseudomonas and showed similarities lower than 95 % in almost all cases with respect to the above species. Cells possessed two polar flagella. The respiratory quinone was Q9. The major fatty acids were C16 : 0, C18 : 1v7c and summed feature 3 (C16 : 1v7c/iso-C15 : 0 2-OH). -
Xylella Fastidiosa Biologia I Epidemiologia
Xylella fastidiosa Biologia i epidemiologia Emili Montesinos Seguí Catedràtic de Producció Vegetal (Patologia Vegetal) Universitat de Girona [email protected] www.youtube.com/watch?v=sur5VzJslcM Xylella fastidiosa, un patogen que no és nou Newton B. Pierce (1890s, USA) Agrobacterium tumefaciens Chlamydiae Proteobacteria Bartonella bacilliformis Campylobacter coli Bartonella henselae CDC Chlamydophila psittaci Campylobacter fetus Bartonella quintana Bacteroides fragilis CDC Brucella melitensis Bacteroidetes Chlamydophila pneumoniae Campylobacter hyointestinalis Bacteroides thetaiotaomicron Campylobacter jejuni CDC Brucella melitensis biovar Abortus CDC Chlamydia trachomatis Capnocytophaga canimorus Campylobacter lari CDC Brucella melitensis biovar Canis Chryseobacterium meningosepticum Parachlamydia acanthamoebae Campylobacter upsaliensis CDC Brucella melitensis biovar Suis Helicobacter pylori Candidatus Liberibacter africanus CDC Candidatus Liberibacter asiaticus Borrelia burgdorferi Epsilon Borrelia hermsii CDC Anaplasma phagocytophilum Borrelia recurrentis Alpha CDC Ehrlichia canis Spirochetes Borrelia turicatae CDC Ehrlichia chaffeensis Eikenella corrodens Leptospira interrogans CDC Ehrlichia ewingii CDC CDC Neisseria gonorrhoeae Treponema pallidum Ehrlichia ruminantium CDC Neisseria meningitidis CDC Neorickettsia sennetsu Spirillum minus Orientia tsutsugamushi Fusobacterium necrophorum Beta Fusobacteria CDC Bordetella pertussis Rickettsia conorii Streptobacillus moniliformis Burkholderia cepacia Rickettsia -
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. -
Characterisation of Pseudomonas Spp. Isolated from Foods
07.QXD 9-03-2007 15:08 Pagina 39 Annals of Microbiology, 57 (1) 39-47 (2007) Characterisation of Pseudomonas spp. isolated from foods Laura FRANZETTI*, Mauro SCARPELLINI Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, sezione Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy Received 30 June 2006 / Accepted 27 December 2006 Abstract - Putative Pseudomonas spp. (102 isolates) from different foods were first characterised by API 20NE and then tested for some enzymatic activities (lipase and lecithinase production, starch hydrolysis and proteolytic activity). However subsequent molecular tests did not always confirm the results obtained, thus highlighting the limits of API 20NE. Instead RFLP ITS1 and the sequencing of 16S rRNA gene grouped the isolates into 6 clusters: Pseudomonas fluorescens (cluster I), Pseudomonas fragi (cluster II and V) Pseudomonas migulae (cluster III), Pseudomonas aeruginosa (cluster IV) and Pseudomonas chicorii (cluster VI). The pectinolytic activity was typical of species isolated from vegetable products, especially Pseudomonas fluorescens. Instead Pseudomonas fragi, predominantly isolated from meat was characterised by proteolytic and lipolytic activities. Key words: Pseudomonas fluorescens, enzymatic activity, ITS1. INTRODUCTION the most frequently found species, however the species dis- tribution within the food ecosystem remains relatively The genus Pseudomonas is the most heterogeneous and unknown (Arnaut-Rollier et al., 1999). The principal micro- ecologically significant group of known bacteria, and bial population of many vegetables in the field consists of includes Gram-negative motile aerobic rods that are wide- species of the genus Pseudomonas, especially the fluores- spread throughout nature and characterised by elevated cent forms. -
High Quality Draft Genome Sequence of the Type Strain of Pseudomonas
Kwak et al. Standards in Genomic Sciences (2016) 11:51 DOI 10.1186/s40793-016-0173-7 SHORT GENOME REPORT Open Access High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T,a phosphate-solubilizing rhizospheric bacterium Yunyoung Kwak, Gun-Seok Park and Jae-Ho Shin* Abstract Pseudomonas lutea OK2T (=LMG 21974T, CECT 5822T) is the type strain of the species and was isolated from the rhizosphere of grass growing in Spain in 2003 based on its phosphate-solubilizing capacity. In order to identify the functional significance of phosphate solubilization in Pseudomonas Plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain OK2T along with its high-quality draft genome sequence, its annotation, and analysis. The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence includes 4,846 protein-coding genes and 95 RNA genes. Keywords: Pseudomonad, Phosphate-solubilizing, Plant growth promoting rhizobacteria (PGPR), Biofertilizer Abbreviations: HGAP, Hierarchical genome assembly process; IMG-ER, Integrated microbial genomes-expert review; KO, Kyoto encyclopedia of genes and genomes Orthology; PGAP, Prokaryotic genome annotation pipeline; PGPR, Plant growth-promoting rhizobacteria; RAST, Rapid annotation using subsystems technology; SMRT, Single molecule real-time Introduction promote plant development by facilitating direct and in- Phosphorus, one of the major essential macronutrients direct plant growth promotion through the production of for plant growth and development, is usually found in phytohormones and enzymes or through the suppression insufficient quantities in soil because of its low solubility of soil-borne diseases by inducing systemic resistance in and fixation [1, 2]. -
Control of Phytopathogenic Microorganisms with Pseudomonas Sp. and Substances and Compositions Derived Therefrom
(19) TZZ Z_Z_T (11) EP 2 820 140 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: A01N 63/02 (2006.01) A01N 37/06 (2006.01) 10.01.2018 Bulletin 2018/02 A01N 37/36 (2006.01) A01N 43/08 (2006.01) C12P 1/04 (2006.01) (21) Application number: 13754767.5 (86) International application number: (22) Date of filing: 27.02.2013 PCT/US2013/028112 (87) International publication number: WO 2013/130680 (06.09.2013 Gazette 2013/36) (54) CONTROL OF PHYTOPATHOGENIC MICROORGANISMS WITH PSEUDOMONAS SP. AND SUBSTANCES AND COMPOSITIONS DERIVED THEREFROM BEKÄMPFUNG VON PHYTOPATHOGENEN MIKROORGANISMEN MIT PSEUDOMONAS SP. SOWIE DARAUS HERGESTELLTE SUBSTANZEN UND ZUSAMMENSETZUNGEN RÉGULATION DE MICRO-ORGANISMES PHYTOPATHOGÈNES PAR PSEUDOMONAS SP. ET DES SUBSTANCES ET DES COMPOSITIONS OBTENUES À PARTIR DE CELLE-CI (84) Designated Contracting States: • O. COUILLEROT ET AL: "Pseudomonas AL AT BE BG CH CY CZ DE DK EE ES FI FR GB fluorescens and closely-related fluorescent GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO pseudomonads as biocontrol agents of PL PT RO RS SE SI SK SM TR soil-borne phytopathogens", LETTERS IN APPLIED MICROBIOLOGY, vol. 48, no. 5, 1 May (30) Priority: 28.02.2012 US 201261604507 P 2009 (2009-05-01), pages 505-512, XP55202836, 30.07.2012 US 201261670624 P ISSN: 0266-8254, DOI: 10.1111/j.1472-765X.2009.02566.x (43) Date of publication of application: • GUANPENG GAO ET AL: "Effect of Biocontrol 07.01.2015 Bulletin 2015/02 Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere (73) Proprietor: Marrone Bio Innovations, Inc. -
Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P
www.nature.com/scientificreports OPEN Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P. Garay3, Jose Manuel Martí3 Accepted: 17 November 2015 & Manuel Porcar1,2 Published: 16 December 2015 We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. There is a growing interest on disentangling the complexity of microbial interactions in order to both optimize reactions performed by natural consortia and to pave the way towards the development of synthetic consor- tia with improved biotechnological properties1,2. Despite the enormous amount of metagenomic data on both natural and artificial microbial ecosystems, bacterial consortia are not necessarily deduced from those data. In fact, the flexibility of the bacterial interactions, the lack of replicated assays and/or biases associated with differ- ent DNA isolation technologies and taxonomic bioinformatics tools hamper the clear identification of bacterial consortia. We propose here a holistic approach aiming at identifying bacterial interactions in laboratory-selected microbial complex cultures. The method requires multi-replicated taxonomic data on independent subcultures, and high-throughput sequencing-based taxonomic data. From this data matrix, randomness of replicates can be verified, linear correlations can be visualized and interactions can emerge from statistical correlations. -
Revisiting the Genomic Structure of the Genus Pseudomonas
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.172809; this version posted May 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into Diversity and Host-related Genetic Determinants Buqing Yi 1* and Alexander H. Dalpke 1 1. Institute of Medical Microbiology and Virology, Medical Faculty, Technical University Dresden, Dresden, Germany *Correspondence: Dr Buqing Yi, Institute of Medical Microbiology and Virology, Medical Faculty, Technical University Dresden, Dresden, Germany. Fetscherstraße 74, 01307 Dresden, Germany, Tel.: +49 351 4586440, Email: [email protected] Keywords: Pseudomonas, opportunistic human pathogen, pan-genome, host-pathogen interaction, antibiotics bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.172809; this version posted May 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. -
University of Groningen Pseudomonas As a Microbial Enzyme Factory Krzeslak, Joanna Kamila
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Groningen University of Groningen Pseudomonas as a microbial enzyme factory Krzeslak, Joanna Kamila IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2009 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Krzeslak, J. K. (2009). Pseudomonas as a microbial enzyme factory: the source of industrially potent enzymes and the host for heterologous enzyme production. Groningen: s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 12-11-2019 CCHAPTER 33 Lipase expression in Pseudomonas alcaligenes is under the control of a two-component regulatory system Joanna Krzeslak, Gijs Gerritse, Ronald van Merkerk, Robbert H. Cool, and Wim J. Quax Appl.