Pseudomonas Diversity Within Urban Freshwaters
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토양에서 분리한 국내 미기록종 Pseudomonas 속 6종의 생화학적 특성과 계통 분류
Korean Journal of Microbiology (2019) Vol. 55, No. 1, pp. 39-45 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2019.8099 eISSN 2383-9902 Copyright ⓒ 2019, The Microbiological Society of Korea 토양에서 분리한 국내 미기록종 Pseudomonas 속 6종의 생화학적 특성과 계통 분류 김현중1 ・ 정유정2 ・ 김해영1 ・ 허문석2* 1 2 경희대학교 생명과학대학 식품생명공학 전공, 국립생물자원관 생물자원연구부 미생물자원과 Isolation and characterization of 6 unrecorded Pseudomonas spp. from Korean soil 1 2 1 2 Hyun-Joong Kim , You-Jung Jung , Hae-Yeong Kim , and Moonsuk Hur * 1 Institute of Life Sciences and Resources Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea 2 Biological Resources Research Department, National Institute of Biological Resources, Incheon 22689, Republic of Korea (Received November 30, 2018; Revised December 19, 2018; Accepted December 19, 2018) In 2017, as a study to discover indigenous prokaryotic species 물의 공통된 특징은 그람 음성(Gram-negative), 호기성, Oxidase in Korea, a total of 6 bacterial strains assigned to the genus 양성 또는 음성, Catalase 양성, 형태학적으로 간균의 모양을 Pseudomonas were isolated from soil. From the high 16S 하고 있다. DNA의 GC 함량은 58~69 mol%이며 하나 혹은 몇 rRNA gene sequence similarity (≥ 99.5%) and phylogenetic 개의 극편모(polar flagella)를 이용하여 운동성을 갖는 것으로 analysis with closely related species, the isolated strains were 알려져 있으며, 현재까지 총 253개 종이 보고 되어 있다(http:// identified as independent Pseudomonas species which were unrecorded in Korea. The six Pseudomonas species were www.bacterio.net/pseudomonas.html) (Palleroni, 1984; Peix Pseudomonas mandelii, P. canadensis, P. thivervalensis, P. et al., 2009; Mulet et al., 2010). -
Which Organisms Are Used for Anti-Biofouling Studies
Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E. -
Università Degli Studi Di Padova Dipartimento Di Biomedicina Comparata Ed Alimentazione
UNIVERSITÀ DEGLI STUDI DI PADOVA DIPARTIMENTO DI BIOMEDICINA COMPARATA ED ALIMENTAZIONE SCUOLA DI DOTTORATO IN SCIENZE VETERINARIE Curriculum Unico Ciclo XXVIII PhD Thesis INTO THE BLUE: Spoilage phenotypes of Pseudomonas fluorescens in food matrices Director of the School: Illustrious Professor Gianfranco Gabai Department of Comparative Biomedicine and Food Science Supervisor: Dr Barbara Cardazzo Department of Comparative Biomedicine and Food Science PhD Student: Andreani Nadia Andrea 1061930 Academic year 2015 To my family of origin and my family that is to be To my beloved uncle Piero Science needs freedom, and freedom presupposes responsibility… (Professor Gerhard Gottschalk, Göttingen, 30th September 2015, ProkaGENOMICS Conference) Table of Contents Table of Contents Table of Contents ..................................................................................................................... VII List of Tables............................................................................................................................. XI List of Illustrations ................................................................................................................ XIII ABSTRACT .............................................................................................................................. XV ESPOSIZIONE RIASSUNTIVA ............................................................................................ XVII ACKNOWLEDGEMENTS .................................................................................................... -
(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. -
Mitigating Biofouling on Reverse Osmosis Membranes Via Greener Preservatives
Mitigating biofouling on reverse osmosis membranes via greener preservatives by Anna Curtin Biology (BSc), Le Moyne College, 2017 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF APPLIED SCIENCE in the Department of Civil Engineering, University of Victoria © Anna Curtin, 2020 University of Victoria All rights reserved. This Thesis may not be reproduced in whole or in part, by photocopy or other means, without the permission of the author. Supervisory Committee Mitigating biofouling on reverse osmosis membranes via greener preservatives by Anna Curtin Biology (BSc), Le Moyne College, 2017 Supervisory Committee Heather Buckley, Department of Civil Engineering Supervisor Caetano Dorea, Department of Civil Engineering, Civil Engineering Departmental Member ii Abstract Water scarcity is an issue faced across the globe that is only expected to worsen in the coming years. We are therefore in need of methods for treating non-traditional sources of water. One promising method is desalination of brackish and seawater via reverse osmosis (RO). RO, however, is limited by biofouling, which is the buildup of organisms at the water-membrane interface. Biofouling causes the RO membrane to clog over time, which increases the energy requirement of the system. Eventually, the RO membrane must be treated, which tends to damage the membrane, reducing its lifespan. Additionally, antifoulant chemicals have the potential to create antimicrobial resistance, especially if they remain undegraded in the concentrate water. Finally, the hazard of chemicals used to treat biofouling must be acknowledged because although unlikely, smaller molecules run the risk of passing through the membrane and negatively impacting humans and the environment. -
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. -
(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. -
The Impact of the Pathogen Rhizoctonia Solani and Its Beneficial Counterpart Bacillus Amyloliquefaciens on the Indigenous Lettuc
ORIGINAL RESEARCH ARTICLE published: 21 April 2014 doi: 10.3389/fmicb.2014.00175 The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome Armin Erlacher 1,2, Massimiliano Cardinale 1,2,RitaGrosch3,MartinGrube2 and Gabriele Berg 1* 1 Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria 2 Institute of Plant Sciences, University of Graz, Graz, Austria 3 Leibniz-Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany Edited by: Lettuce belongs to the most commonly raw eaten food worldwide and its microbiome Kornelia Smalla, Julius Kühn-Institut, plays an important role for both human and plant health. Yet, little is known about the Germany impact of potentially occurring pathogens and beneficial inoculants of the indigenous Reviewed by: microorganisms associated with lettuce. To address this question we studied the impact Zuhua He, Chinese Academy of Sciences, China of the phytopathogenic fungus Rhizoctonia solani and the biological control agent Bacillus Franz Narberhaus, Ruhr University amyloliquefaciens FZB42 on the indigenous rhizosphere and phyllosphere community Bochum, Germany of greenhouse-grown lettuce at two plant stages. The rhizosphere and phyllosphere Kornelia Smalla, Julius Kühn-Institut, gammaproteobacterial microbiomes of lettuce plants showed clear differences in their Germany Monica Höfte, Ghent University, overall and core microbiome composition as well as in corresponding diversity indices. The -
An Insight Into Beneficial Pseudomonas Bacteria
Chapter 5 An Insight Into Beneficial Pseudomonas bacteria Galina Novik, Victoria Savich and Elena Kiseleva Additional information is available at the end of the chapter http://dx.doi.org/10.5772/60502 Abstract Pseudomonas is a widespread bacterial genus embracing a vast number of species. Various genosystematic methods are used to identify Pseudomonas and differentiate these bacteria from species of the same genus and species of other genera. Ability to degrade and produce a whole spectrum of compounds makes these species perspec‐ tive in industrial applications. It also makes possible to use various media, including wastes, for cultivation of Pseudomonas. Pseudomonads may be applied in bioreme‐ diation, production of polymers and low-molecular-weight compounds, biocontrol. Recent studies open up new frontiers for further use of Pseudomonas in various areas. Keywords: Pseudomonas bacteria, physiology, taxonomy, application 1. Introduction Pseudomonas is one of the most studied species of bacteria. They were first identified at the end of 19th century by Migula as Gram-negative, rod-shaped and polar-flagellated bacteria. Since that time description of genus Pseudomonas has widened; development of new methods allowed to study in detail the morphology and physiology of these bacteria. However, the morphological characteristics of Pseudomonas are common to many bacterial genera and so are of little value in the positive identification of members of the genus. Advanced nucleic acid- based methods allow to differentiate it from other similar genera and reveal taxonomic relationships among various bacterial species including Pseudomonas. Genus Pseudomonas is represented by species that occupy a wide range of niches owing to metabolic and physiological diversity. -
Draft Genome Sequence of Pseudomonas Moraviensis Strain Devor Implicates Metabolic Versatility and Bioremediation Potential
Genomics Data 9 (2016) 154–159 Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential Neil T. Miller a,DannyFullera,M.B.Cougera, Mark Bagazinski a,PhilipBoynea, Robert C. Devor a, Radwa A. Hanafy a, Connie Budd a, Donald P. French b, Wouter D. Hoff a, Noha Youssef a,⁎ a Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States b Department of Integrative Biology, Oklahoma State University, Stillwater, OK, United States article info abstract Article history: Pseudomonas moraviensis is a predominant member of soil environments. We here report on the genomic Received 19 July 2016 analysis of Pseudomonas moraviensis strain Devor that was isolated from a gate at Oklahoma State University, Accepted 2 August 2016 Stillwater, OK, USA. The partial genome of Pseudomonas moraviensis strain Devor consists of 6016489 bp of Available online 4 August 2016 DNA with 5290 protein-coding genes and 66 RNA genes. This is the first detailed analysis of a P. moraviensis genome. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport Keywords: of fructose, xylose, mannose and all amino acids with the exception of tryptophan and valine, implying that Pseudomonas moraviensis Draft genome sequence the organism is a versatile heterotroph. The genome of P. moraviensis strain Devor was rich in transporters Detailed analysis and, based on COG analysis, did not cluster closely with P. moraviensis R28-S genome, the only previous report Student Initiated Microbial Discovery (SIMD) of a P. -
Microbial Diversity and Soil Physiochemical Characteristic of Higher Altitude
RESEARCH ARTICLE Microbial diversity and soil physiochemical characteristic of higher altitude 1 1 2 2 1 Saurabh KumarID *, Deep Chandra Suyal , Amit Yadav , Yogesh Shouche , Reeta Goel 1 Department of Microbiology, College of Basic Sciences and Humanities; Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India, 2 National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, India * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 a1111111111 Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical pro- perties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal soil. Soil phy- siochemical analysis showed that altitude was positively correlated with soil pH, organic OPEN ACCESS matter and total nitrogen content. However soil mineral nutrients and soil phosphorus were Citation: Kumar S, Suyal DC, Yadav A, Shouche Y, negatively correlated to the altitude. RT-PCR based analysis revealed the decreased bacte- Goel R (2019) Microbial diversity and soil physiochemical characteristic of higher altitude. rial and diazotrophic abundance at high altitude. Metagenomic study showed that Proteo- PLoS ONE 14(3): e0213844. https://doi.org/ bacteria, Acidobacteria and Actinobacteria were dominant bacteria phyla at high altitude soil 10.1371/journal.pone.0213844 while Bacteroidetes and Fermicutes were found dominant at low altitude. High ratio of Editor: Pankaj Kumar Arora, Babasaheb Bhimrao Gram-negative to Gram positive bacteria at Gangotri suggests the selective proliferation of Ambedkar University, INDIA Gram negative bacteria at high altitude with decrease in Gram positive bacteria.