Pseudomonas Jicuserectae Sp. Nov., the Causal Agent of Bacterial Leaf Spot of Ficus Erecta Thunb
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Estudio Molecular De Poblaciones De Pseudomonas Ambientales
Universitat de les Illes Balears ESTUDIO MOLECULAR DE POBLACIONES DE PSEUDOMONAS AMBIENTALES T E S I S D O C T O R A L DAVID SÁNCHEZ BERMÚDEZ DIRECTORA: ELENA GARCÍA-VALDÉS PUKKITS Departamento de Biología Universitat de les Illes Balears Palma de Mallorca, Septiembre 2013 Universitat de les Illes Balears ESTUDIO MOLECULAR DE POBLACIONES DE PSEUDOMONAS AMBIENTALES Tesis Doctoral presentada por David Sánchez Bermúdez para optar al título de Doctor en el programa Microbiología Ambiental y Biotecnología, de la Universitat de les Illes Balears, bajo la dirección de la Dra. Elena García-Valdés Pukkits. Vo Bo Director de la Tesis El doctorando DRA. ELENA GARCÍA-VALDÉS PUKKITS DAVID SÁNCHEZ BERMÚDEZ Catedrática de Universidad Universitat de les Illes Balears PALMA DE MALLORCA, SEPTIEMBRE 2013 III IV Index Agradecimientos .................................................................................................... IX Resumen ................................................................................................................ 1 Abstract ................................................................................................................... 3 Introduction ............................................................................................................ 5 I.1. The genus Pseudomonas ............................................................................................ 7 I.1.1. Definition ................................................................................................................ 7 I.1.2. -
Microbiological Quality and Occurrence of Antibiotic Resistant Bacteria in Ready-To-Eat Salad
Microbiological quality and occurrence of antibiotic resistant bacteria in ready-to-eat salad Tamara Lupan Master thesis for a diploma in Food Technology and Nutrition, 30 ECTS credits Department of Food Technology, Engineering and Nutrition, Faculty of Engineering, Lund University Abstract An increase in demand for fresh vegetables resulted in an increased production of minimally processed, ready-to-eat salad in Sweden. That also brought new food safety challenges that are yet to be addressed. To assess whether ready-to-eat leafy green vegetables present a threat in terms of food borne outbreaks, aerobic bacteria, as well as bacteria belonging to the Enterobacteriaceae family, were recovered, using selective media, from 3 different sets (n=18) of ready-to-eat rocket salad. Bacterial investigation showed that most bacteria retrieved from ready-to-eat rocket salad belongs to the Pseudomonadaceae family, which are typical spoilage bacteria commonly associated with vegetables. No food-borne pathogens (e.g. Clostridium botulinum, Escherichia coli O157:H7, Salmonella spp., Shigella spp., Listeria monocytogenes) were isolated from any of three sets of rocket salad. Following the assumption that microbiological quality of the salad could change during the storage period, as well as a result of salad bags being opened, sealed, stored and opened again in the household, the total aerobic count as well as the total amount of Enterobacteriaceae were assessed every day before the best-before date. Following the NSW food Authority guidance on the microbiological status of ready-to-eat food, it can be confirmed, that each of three sets of salad were from the first day after packaging, unsatisfactory in regards to total aerobic count, showing values higher than 5 log CFU/g. -
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
Host Specificity and Virulence of the Phytopathogenic Bacteria Pseudomonas Savastanoi Eloy Caballo Ponce Caballo Eloy
Host specificity and virulence of the phytopathogenic bacteria Pseudomonas savastanoi Eloy Caballo Ponce Caballo Eloy TESIS DOCTORAL Eloy Caballo Ponce Director: Cayo Ramos Rodríguez Programa de Doctorado: Biotecnología Avanzada TESIS DOCTORAL TESIS Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” Universidad de Málaga – CSIC 2017 Año 2017 Memoria presentada por: Eloy Caballo Ponce para optar al grado de Doctor por la Universidad de Málaga Host specificity and virulence of the phytopathogenic bacteria Pseudomonas savastanoi Director: Cayo J. Ramos Rodríguez Catedrático. Área de Genética. Departamento de Biología Celular, Genética y Fisiología. Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM) Universidad de Málaga – Consejo Superior de Investigaciones Científicas Málaga, 2016 AUTOR: Eloy Caballo Ponce http://orcid.org/0000-0003-0501-3321 EDITA: Publicaciones y Divulgación Científica. Universidad de Málaga Esta obra está bajo una licencia de Creative Commons Reconocimiento-NoComercial- SinObraDerivada 4.0 Internacional: http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode Cualquier parte de esta obra se puede reproducir sin autorización pero con el reconocimiento y atribución de los autores. No se puede hacer uso comercial de la obra y no se puede alterar, transformar o hacer obras derivadas. Esta Tesis Doctoral está depositada en el Repositorio Institucional de la Universidad de Málaga (RIUMA): riuma.uma.es COMITÉ EVALUADOR Presidente Dr. Jesús Murillo Martínez Departamento de Producción Agraria Universidad Pública de Navarra Secretario Dr. Francisco Manuel Cazorla López Departamento de Microbiología Universidad de Málaga Vocal Dra. Chiaraluce Moretti Departamento de Ciencias Agrarias, Alimentarias y Medioambientales Universidad de Perugia Suplentes Dr. Pablo Rodríguez Palenzuela Departamento de Biotecnología – Biología Vegetal Universidad Politécnica de Madrid Dr. -
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. -
(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. -
Phenotypic and Genetic Diversity of Pseudomonads
PHENOTYPIC AND GENETIC DIVERSITY OF PSEUDOMONADS ASSOCIATED WITH THE ROOTS OF FIELD-GROWN CANOLA A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon By Danielle Lynn Marie Hirkala © Copyright Danielle Lynn Marie Hirkala, November 2006. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon, Saskatchewan, S7N 5A8 i ABSTRACT Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. -
Aquatic Microbial Ecology 80:15
The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package. -
(12) United States Patent (10) Patent No.: US 7,618,799 B2 Coleman Et Al
US007618799B2 (12) United States Patent (10) Patent No.: US 7,618,799 B2 Coleman et al. (45) Date of Patent: Nov. 17, 2009 (54) BACTERIAL LEADER SEQUENCES FOR NCBI Report for Accession No.YP 346180, Direct Submission on INCREASED EXPRESSION Aug. 8, 2005. Huber, D., “Use of Thioredoxin as a Reporter to Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition (75) Inventors: Russell J. Coleman, San Diego, CA Particle-Dependent Translocation.” Journal of Bacteriology, 2005, (US); Diane Retallack, Poway, CA pp. 2983-2991, vol. 187 (9). (US); Jane C. Schneider, San Diego, Miot, M. and Betton, J., “Protein Quality Control in the Bacterial CA (US); Thomas M. Ramseier, Periplasm.” Microbial Cell Factories, 2004, pp. 1-13. Newton, MA (US); Charles D. Ma, Q., et al., “Protein Secretion Systems of Pseudomonas Hershberger, Poway, CA (US); Stacey aeruginosa and Pfluorescens.” Biochim. Biophys. Acta, Apr. 1, 2003, Lee, San Diego, CA (US): Sol M. pp. 223-233, vol. 1611, No. 1-2. Resnick, Encinitas, CA (US) Retallack, D.M., et al..."Transport of Heterologous Proteins to the Periplasmic Space of Pseudomonas fluorescens Using a Variety of (73) Assignee: Dow Global Technologies Inc, Midland, Native Signal Sequences, ’’ Biotechnol Lett, Oct. 2007, pp. 1483 MI (US) 1491, vol. 29, No. 10. Urban, A., et al., “DsbA and DsbC Affect Extracellular Enzyme Formation in Pseudomonas aeruginosa. J. Bacteriol. Jan. 2001, pp. (*) Notice: Subject to any disclaimer, the term of this 587-596, vol. 183, No. 2. patent is extended or adjusted under 35 Wang, H., et al., “High-level Expression of Human TFF3 in U.S.C. -
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. -
Pathogen Profile
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Academica-e MOLECULAR PLANT PATHOLOGY (2012) 13(9), 998–1009 DOI: 10.1111/j.1364-3703.2012.00816.x Pathogen profile Pseudomonas savastanoi pv. savastanoi: Some like it knot Cayo Ramos1, Isabel M. Matas1, Leire Bardaji2, Isabel M. Aragón1, Jesús Murillo2* 1 Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Área de Genética, Facultad de Ciencias, Campus Teatinos s/n, E-29010 Málaga, Spain 2 Departamento de Producción Agraria, ETS Ingenieros Agrónomos, Universidad Pública de Navarra, 31006 Pamplona, Spain * Corresponding author: Jesús Murillo; [email protected] Key words: Pseudomonas syringae pv. savastanoi, olive knot, tumour, genome sequencing, plant disease, control, pathogenicity, virulence, effector. SUMMARY molecular biology that has elevated the foliar pathogens of the P. syringae complex to Pseudomonas savastanoi pv. savastanoi is the supermodels. A series of studies in the last years causal agent of olive (Olea europaea) knot have made significant advances in the biology, disease and an unorthodox member of the P. ecology and genetics of P. savastanoi pv. syringae complex, causing aerial tumours instead savastanoi, paving the way for the molecular of the foliar necroses and cankers characteristic dissection of its interaction with other non- of most members of this complex. Olive knot is pathogenic bacteria and their woody hosts. The present wherever olive is grown; although losses selection of a genetically pliable model strain was are difficult to assess, it is assumed that olive knot soon followed by the development of rapid is one of the most important diseases of the olive methods for virulence assessment with crop. -
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.