Pseudomonas Versuta Sp. Nov., Isolated from Antarctic Soil
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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). -
Molecular Analysis of the Bacterial Communities in Crude Oil Samples from Two Brazilian Offshore Petroleum Platforms
Hindawi Publishing Corporation International Journal of Microbiology Volume 2012, Article ID 156537, 8 pages doi:10.1155/2012/156537 Research Article Molecular Analysis of the Bacterial Communities in Crude Oil Samples from Two Brazilian Offshore Petroleum Platforms Elisa Korenblum,1 Diogo Bastos Souza,1 Monica Penna,2 and Lucy Seldin1 1 Laborat´orio de Gen´etica Microbiana, Instituto de Microbiologia Prof. Paulo de G´oes, Universidade Federal do Rio de Janeiro, Centro de Ciˆencias da Sa´ude, Bloco I, Ilha do Fund˜ao, 21941-590 Rio de Janeiro, RJ, Brazil 2 Gerˆencia de Biotecnologia e Tratamentos Ambientais, CENPES-PETROBRAS, Ilha do Fund˜ao, 21949-900 Rio de Janeiro, RJ, Brazil Correspondence should be addressed to Lucy Seldin, [email protected] Received 18 April 2011; Revised 11 June 2011; Accepted 13 October 2011 Academic Editor: J. Wiegel Copyright © 2012 Elisa Korenblum et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Crude oil samples with high- and low-water content from two offshore platforms (PA and PB) in Campos Basin, Brazil, were assessed for bacterial communities by 16S rRNA gene-based clone libraries. RDP Classifier was used to analyze a total of 156 clones within four libraries obtained from two platforms. The clone sequences were mainly affiliated with Gammaproteobacteria (78.2% of the total clones); however, clones associated with Betaproteobacteria (10.9%), Alphaproteobacteria (9%), and Firmicutes (1.9%) were also identified. Pseudomonadaceae was the most common family affiliated with these clone sequences. -
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. -
Evolutionary Patchwork of an Insecticidal Toxin
Ruffner et al. BMC Genomics (2015) 16:609 DOI 10.1186/s12864-015-1763-2 RESEARCH ARTICLE Open Access Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus Beat Ruffner1, Maria Péchy-Tarr2, Monica Höfte3, Guido Bloemberg4, Jürg Grunder5, Christoph Keel2* and Monika Maurhofer1* Abstract Background: Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling. Results: Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster. Conclusions: Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution. -
Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
Pseudomonas Chlororaphis PA23 Biocontrol of Sclerotinia Sclerotiorum on Canola
Pseudomonas chlororaphis PA23 Biocontrol of Sclerotinia sclerotiorum on Canola: Understanding Populations and Enhancing Inoculation LORI M. REIMER A Thesis Submitted to the Faculty of Graduate Studies In Partial Fulfillment of the Requirements For the Degree of MASTER OF SCIENCE Department of Plant Science University of Manitoba Winnipeg, Manitoba © Copyright by Lori M. Reimer 2016 GENERAL ABSTRACT Reimer, Lori M. M.Sc., The University of Manitoba, June 2016. Pseudomonas chlroraphis PA23 Biocontrol of Sclerotinia sclerotiorum on Canola: Understanding Populations and Enhancing Inoculation. Supervisor, Dr. Dilantha Fernando. Pseudomonas chlororaphis strain PA23 has demonstrated biocontrol of Sclerotinia sclerotiorum (Lib.) de Bary, a fungal pathogen of canola (Brassica napus L.). This biocontrol is mediated through the production of secondary metabolites, of which the antibiotics pyrrolnitrin and phenazine are major contributers. The objectives of this research were two-fold: to optimize PA23 phyllosphere biocontrol and to investigate PA23’s influence in the rhizosphere. PA23 demonstrated longevity, both in terms of S. sclerotiorum biocontrol and by having viable cells after 7 days, when inoculated on B. napus under greenhouse conditions. Carbon source differentially effected growth rate and antifungal metabolite production of PA23 in culture. PA23 grew fasted in glucose and glycerol, while mannose lead to the greatest inhibition of S. sclerotiorum mycelia and fructose lead to the highest levels of antibiotic production relative to cell density. Carbon source did not have a significant effect on in vivo biocontrol. PA23 demonstrated biocontrol ability of the fungal root pathogens Rhizoctonia solani J.G. Kühn and Pythium ultimum Trow in radial diffusion assays. PA23’s ability to promote seedling root growth was demonstrated in sterile growth pouches, but in a soil system these results were reversed. -
Pseudomonas Populations Causing Pith Necrosis of Tomato and Pepper in Argentina Are Highly Diverse
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by SEDICI - Repositorio de la UNLP Plant Pathology (2003) 52, 287-302 Pseudomonas populations causing pith necrosis of tomato and pepper in Argentina are highly diverse A. M. Alippia*t, E. Dal Boa, L. B. Ronco3, M. V. Lópezb, A. C. Lópezb and O. M. Aguilarb sCentro de Investigaciones de Fitopatología, Facultad de Cs. Agrarias y Forestales, Universidad Nacional de La Plata, c.c. 31, calles 60 y 118, 1900 La Plata; andbInstituto de Bioguímica y Biología Molecular, Facultad de Cs. Exactas, UNLP, calles 47 y 115, 1900 La Plata, Argentina Pseudomonas species causing pith necrosis symptoms on tomato and pepper collected in different areas of Argentina were identified as Pseudomonas corrugata, P. viridiflava and Pseudomonas spp. Their diversity was analysed and compared with reference strains on the basis of their phenotypic characteristics, copper and antibiotic sensitivity tests, serology, pathogenicity, DNA fingerprinting and restriction fragment length polymorphism (RFLP) analysis of a 16S rRNA gene fragment. All P. corrugata strains tested were copper-resistant while P. viridiflava strains were more variable. Numerical analysis of phenotypic data showed that all P. corrugata strains formed a single phenon that clustered at a level of about 93%, while all the P. viridiflava strains clustered in a separated phenon at a level of 94%. Genomic analysis by repetitive (rep)-PCR and 16S rRNA-RFLP fingerprinting and serological analysis showed that the two species contained considerable genetic diversity. Inoculations of tomato and pepper plants with strains from both hosts caused similar pith necrosis symptoms. -
Symbiotic Bacteria Associated with Ascidian Vanadium Accumulation Identified by 16S Rrna Amplicon Sequencing
Symbiotic bacteria associated with ascidian vanadium accumulation identified by 16S rRNA amplicon sequencing Author Tatsuya Ueki, Manabu Fujie, Romaidi, Noriyuki Satoh journal or Marine Genomics publication title volume 43 page range 33-42 year 2018-11-09 Publisher Elsevier B.V. Rights (C) 2018 The Author(s). Author's flag publisher URL http://id.nii.ac.jp/1394/00000917/ doi: info:doi/10.1016/j.margen.2018.10.006 Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (https://creativecommons.org/licenses/by-nc-nd/4.0/) Marine Genomics 43 (2019) 33–42 Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Full length article Symbiotic bacteria associated with ascidian vanadium accumulation identified by 16S rRNA amplicon sequencing T ⁎ Tatsuya Uekia,b, , Manabu Fujiec, Romaidia,d, Noriyuki Satohe a Molecular Physiology Laboratory, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan b Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima, Japan c DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan d Biology Department, Science and Technology Faculty, State Islamic University of Malang, Malang, Jawa Timur, Indonesia e Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan ARTICLE INFO ABSTRACT Keywords: Ascidians belonging to Phlebobranchia accumulate vanadium to an extraordinary degree (≤ 350 mM). Bacterial population Vanadium levels are strictly regulated and vary among ascidian species; thus, they represent well-suited models 16S rRNA for studies on vanadium accumulation. No comprehensive study on metal accumulation and reduction in marine Marine invertebrates organisms in relation to their symbiotic bacterial communities has been published. -
Genomic Analysis of Three Cheese-Borne Pseudomonas Lactis with Biofilm and Spoilage-Associated Behavior
microorganisms Article Genomic Analysis of Three Cheese-Borne Pseudomonas lactis with Biofilm and Spoilage-Associated Behavior Laura Quintieri 1 , Leonardo Caputo 1,* , Maria De Angelis 2 and Francesca Fanelli 1 1 Institute of Sciences of Food Production, National Research Council of Italy, Via G. Amendola 122/O, 70126 Bari, Italy; [email protected] (L.Q.); [email protected] (F.F.) 2 Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-080-592-9323; Fax: +39-080-592-9374 Received: 10 July 2020; Accepted: 5 August 2020; Published: 8 August 2020 Abstract: Psychrotrophic pseudomonads cause spoilage of cold fresh cheeses and their shelf-life reduction. Three cheese-borne Pseudomonas sp., ITEM 17295, ITEM 17298, and ITEM 17299 strains, previously isolated from mozzarella cheese, revealed distinctive spoilage traits based on molecular determinants requiring further investigations. Genomic indexes (ANI, isDDH), MLST-based phylogeny of four housekeeping genes (16S rRNA, gyrB, rpoB and rpoD) and genome-based phylogeny reclassified them as Pseudomonas lactis. Each strain showed distinctive phenotypic traits at 15 and 30 ◦C: ITEM 17298 was the highest biofilm producer at both temperatures, whilst ITEM 17295 and ITEM 17299 showed the strongest proteolytic activity at 30 ◦C. A wider pattern of pigments was found for ITEM 17298, while ITEM 17295 colonies were not pigmented. Although the high genomic similarity, some relevant molecular differences supported this phenotypic diversity: ITEM 17295, producing low biofilm amount, missed the pel operon involved in EPS synthesis and the biofilm-related Toxin-Antitoxin systems (mqsR/mqsA, chpB/chpS); pvdS, required for the pyoverdine synthesis, was a truncated gene in ITEM 17295, harboring, instead, a second aprA involved in milk proteolysis. -
Rapport Nederlands
Moleculaire detectie van bacteriën in dekaarde Dr. J.J.P. Baars & dr. G. Straatsma Plant Research International B.V., Wageningen December 2007 Rapport nummer 2007-10 © 2007 Wageningen, Plant Research International B.V. Alle rechten voorbehouden. Niets uit deze uitgave mag worden verveelvoudigd, opgeslagen in een geautomatiseerd gegevensbestand, of openbaar gemaakt, in enige vorm of op enige wijze, hetzij elektronisch, mechanisch, door fotokopieën, opnamen of enige andere manier zonder voorafgaande schriftelijke toestemming van Plant Research International B.V. Exemplaren van dit rapport kunnen bij de (eerste) auteur worden besteld. Bij toezending wordt een factuur toegevoegd; de kosten (incl. verzend- en administratiekosten) bedragen € 50 per exemplaar. Plant Research International B.V. Adres : Droevendaalsesteeg 1, Wageningen : Postbus 16, 6700 AA Wageningen Tel. : 0317 - 47 70 00 Fax : 0317 - 41 80 94 E-mail : [email protected] Internet : www.pri.wur.nl Inhoudsopgave pagina 1. Samenvatting 1 2. Inleiding 3 3. Methodiek 8 Algemene werkwijze 8 Bestudeerde monsters 8 Monsters uit praktijkteelten 8 Monsters uit proefteelten 9 Alternatieve analyse m.b.v. DGGE 10 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 11 4. Resultaten 13 Monsters uit praktijkteelten 13 Monsters uit proefteelten 16 Alternatieve analyse m.b.v. DGGE 23 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 25 5. Discussie 28 6. Conclusies 33 7. Suggesties voor verder onderzoek 35 8. Gebruikte literatuur. 37 Bijlage I. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit commerciële teelten I-1 Bijlage II. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit experimentele teelten II-1 1 1.