Systematic Affiliation and Genome Analysis of Subtercola Vilae DB165
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Rhodoglobus Vestalii Gen. Nov., Sp. Nov., a Novel Psychrophilic Organism Isolated from an Antarctic Dry Valley Lake
International Journal of Systematic and Evolutionary Microbiology (2003), 53, 985–994 DOI 10.1099/ijs.0.02415-0 Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake Peter P. Sheridan,1 Jennifer Loveland-Curtze,2 Vanya I. Miteva2 and Jean E. Brenchley2 Correspondence 1Department of Biological Sciences, PO Box 8007, Idaho State University, Pocatello, Vanya I. Miteva ID 83209, USA [email protected] 2Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA A novel, psychrophilic, Gram-positive bacterium (designated strain LV3T) from a lake near the McMurdo Ice Shelf, Antarctica, has been isolated and characterized. This organism formed red-pigmented colonies, had an optimal growth temperature of 18 ˚C and grew on a variety of media between ”2 and 21 ˚C. Scanning electron micrographs of strain LV3T that showed small rods with unusual bulbous protuberances during all phases of growth were of particular interest. The G+C content of the genomic DNA was approximately 62 mol%. The cell walls contained ornithine as the diamino acid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cells grown at ”2 ˚C contained significant amounts of anteiso-C15 : 1. The major menaquinones found in strain LV3T were MK-11 and MK-12. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain LV3T was a member of the family Microbacteriaceae and related to, but distinct from, organisms belonging to the genera Agreia, Leifsonia and Subtercola.In addition, alignments of 16S rRNA sequences showed that the sequence of strain LV3T contained a 13 bp insertion that was found in only a few related sequences. -
Characterization of a Microbial Community Capable of Nitrification At
Bioresource Technology 101 (2010) 491–500 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Characterization of a microbial community capable of nitrification at cold temperature Thomas F. Ducey *, Matias B. Vanotti, Anthony D. Shriner, Ariel A. Szogi, Aprel Q. Ellison Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, 2611 West Lucas Street, Florence, SC 29501, United States article info abstract Article history: While the oxidation of ammonia is an integral component of advanced aerobic livestock wastewater Received 5 February 2009 treatment, the rate of nitrification by ammonia-oxidizing bacteria is drastically reduced at colder temper- Received in revised form 30 July 2009 atures. In this study we report an acclimated lagoon nitrifying sludge that is capable of high rates of nitri- Accepted 30 July 2009 fication at temperatures from 5 °C (11.2 mg N/g MLVSS/h) to 20 °C (40.4 mg N/g MLVSS/h). The Available online 5 September 2009 composition of the microbial community present in the nitrifying sludge was investigated by partial 16S rRNA gene sequencing. After DNA extraction and the creation of a plasmid library, 153 partial length Keywords: 16S rRNA gene clones were sequenced and analyzed phylogenetically. Over 80% of these clones were Nitrite affiliated with the Proteobacteria, and grouped with the b- (114 clones), - (7 clones), and -classes (2 Ammonia-oxidizing bacteria c a Nitrosomonas clones). The remaining clones were affiliated with the Acidobacteria (1 clone), Actinobacteria (8 clones), Activated sludge Bacteroidetes (16 clones), and Verrucomicrobia (5 clones). The majority of the clones belonged to the genus 16S rRNA gene Nitrosomonas, while other clones affiliated with microorganisms previously identified as having floc forming or psychrotolerance characteristics. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 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. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Diversity and Taxonomic Novelty of Actinobacteria Isolated from The
Diversity and taxonomic novelty of Actinobacteria isolated from the Atacama Desert and their potential to produce antibiotics Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Alvaro S. Villalobos Kiel 2018 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: Prof. Dr. Ute Hentschel Humeida Tag der mündlichen Prüfung: Zum Druck genehmigt: 03.12.2018 gez. Prof. Dr. Frank Kempken, Dekan Table of contents Summary .......................................................................................................................................... 1 Zusammenfassung ............................................................................................................................ 2 Introduction ...................................................................................................................................... 3 Geological and climatic background of Atacama Desert ............................................................. 3 Microbiology of Atacama Desert ................................................................................................. 5 Natural products from Atacama Desert ........................................................................................ 9 References .................................................................................................................................. 12 Aim of the thesis ........................................................................................................................... -
Supplement of Screening of Cloud Microorganisms Isolated at the Puy De Dôme (France) Station for the Production of Biosurfactants
Supplement of Atmos. Chem. Phys., 16, 12347–12358, 2016 http://www.atmos-chem-phys.net/16/12347/2016/ doi:10.5194/acp-16-12347-2016-supplement © Author(s) 2016. CC Attribution 3.0 License. Supplement of Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants Pascal Renard et al. Correspondence to: Anne-Marie Delort ([email protected]) The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence. Table S1. Strains are isolated during 39 cloud events (from 2004 to 2014) gathered in four categories according to the physicochemical characteristics of the cloud waters (Blue: marine, purple: highly marine, green: continental and black: polluted) as described by Deguillaume et al. (2014). Cloud Nb of Ions (µM) Composition Date pH 2- - - + + 2+ + 2+ Event strains SO 4 NO 3 Cl Acetate Formate Oxalate Succinate Malonate Na NH 4 Mg K Ca 21 Marine 2 2004-01 5.6 NA NA NA NA NA NA NA NA NA NA NA NA NA 23 Polluted 2 2004-02 3.1 NA NA NA NA NA NA NA NA NA NA NA NA NA 29 Marine 1 2004-07 5.5 NA NA NA NA NA NA NA NA NA NA NA NA NA 30 Marine 3 2004-09 7.6 3.8 6.5 12.0 6.0 6.0 0.5 0.1 0.16 19.4 54.9 4.9 4.1 12.0 32 Continental 1 2004-12 5.5 72.1 95.8 31.5 0.0 0.3 0.3 0.1 0.17 74.4 132.4 7.6 9.0 73.7 42 Continental 25 2007-12 4.7 39.7 198.4 20.2 10.2 5.8 2.9 0.6 0.58 19.1 148.2 3.5 11.9 58.0 43 Highly marine 25 2008-01 5.9 9.4 21.4 81.4 11.4 6.7 1.2 0.2 0.28 315.7 35.9 11.8 13.7 26.0 44 Continental 14 2008-02 5.2 24.6 65.9 17.2 26.8 18.0 1.3 0.5 0.39 -
Report on 31 Unrecorded Bacterial Species in Korea That Belong to the Phylum Actinobacteria
Journal of Species Research 5(1):113, 2016 Report on 31 unrecorded bacterial species in Korea that belong to the phylum Actinobacteria JungHye Choi1, JuHee Cha1, JinWoo Bae2, JangCheon Cho3, Jongsik Chun4, WanTaek Im5, Kwang Yeop Jahng6, Che Ok Jeon7, Kiseong Joh8, Seung Bum Kim9, Chi Nam Seong10, JungHoon Yoon11 and ChangJun Cha1,* 1Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Korea 3Department of Biological Sciences, Inha University, Incheon 22212, Korea 4School of Biological Sciences, Seoul National University, Seoul 08826, Korea 5Department of Biotechnology, Hankyong National University, Anseong 17579, Korea 6Department of Life Sciences, Chonbuk National University, Jeonju-si 54896, Korea 7Department of Life Science, Chung-Ang University, Seoul 06974, Korea 8Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Korea 9Department of Microbiology, Chungnam National University, Daejeon 34134, Korea 10Department of Biology, Sunchon National University, Suncheon 57922, Korea 11Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea *Correspondent: [email protected] To discover and characterize indigenous species in Korea, a total of 31 bacterial strains that belong to the phylum Actinobacteria were isolated from various niches in Korea. Each strain showed the high sequence similarity (>99.1%) with the closest bacterial species, forming a robust phylogenetic clade. These strains have not been previously recorded in Korea. According to the recently updated taxonomy of the phylum Actinobacteria based upon 16S rRNA trees, we report 25 genera of 13 families within 5 orders of the class Actinobacteria as actinobacterial species found in Korea. -
Wild Apple-Associated Fungi and Bacteria Compete to Colonize the Larval Gut of an Invasive Wood-Borer Agrilus Mali in Tianshan Forests
Wild apple-associated fungi and bacteria compete to colonize the larval gut of an invasive wood-borer Agrilus mali in Tianshan forests Tohir Bozorov ( [email protected] ) Xinjiang Institute of Ecology and Geography https://orcid.org/0000-0002-8925-6533 Zokir Toshmatov Plant Genetics Research Unit: Genetique Quantitative et Evolution Le Moulon Gulnaz Kahar Xinjiang Institute of Ecology and Geography Daoyuan Zhang Xinjiang Institute of Ecology and Geography Hua Shao Xinjiang Institute of Ecology and Geography Yusufjon Gafforov Institute of Botany, Academy of Sciences of Uzbekistan Research Keywords: Agrilus mali, larval gut microbiota, Pseudomonas synxantha, invasive insect, wild apple, 16S rRNA and ITS sequencing Posted Date: March 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-287915/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background: The gut microora of insects plays important roles throughout their lives. Different foods and geographic locations change gut bacterial communities. The invasive wood-borer Agrilus mali causes extensive mortality of wild apple, Malus sieversii, which is considered a progenitor of all cultivated apples, in Tianshan forests. Recent analysis showed that the gut microbiota of larvae collected from Tianshan forests showed rich bacterial diversity but the absence of fungal species. In this study, we explored the antagonistic ability of gut bacteria to address this absence of fungi in the larval gut. Results: The results demonstrated that gut bacteria were able to selectively inhibit wild apple tree-associated fungi. However, Pseudomonas synxantha showed strong antagonistic ability, producing antifungal compounds. Using different analytical methods, such as column chromatography, mass spectrometry, HPLC and NMR, an antifungal compound, phenazine-1-carboxylic acid (PCA), was identied. -
To Obtain Approval for Projects to Develop Genetically Modified Organisms in Containment
APPLICATION FORM Containment – GMO Project To obtain approval for projects to develop genetically modified organisms in containment Send to Environmental Protection Authority preferably by email ([email protected]) or alternatively by post (Private Bag 63002, Wellington 6140) Payment must accompany final application; see our fees and charges schedule for details. Application Number APP203205 Date 02/10/2017 www.epa.govt.nz 2 Application Form Approval for projects to develop genetically modified organisms in containment Completing this application form 1. This form has been approved under section 42A of the Hazardous Substances and New Organisms (HSNO) Act 1996. It only covers projects for development (production, fermentation or regeneration) of genetically modified organisms in containment. This application form may be used to seek approvals for a range of new organisms, if the organisms are part of a defined project and meet the criteria for low risk modifications. Low risk genetic modification is defined in the HSNO (Low Risk Genetic Modification) Regulations: http://www.legislation.govt.nz/regulation/public/2003/0152/latest/DLM195215.html. 2. If you wish to make an application for another type of approval or for another use (such as an emergency, special emergency or release), a different form will have to be used. All forms are available on our website. 3. It is recommended that you contact an Advisor at the Environmental Protection Authority (EPA) as early in the application process as possible. An Advisor can assist you with any questions you have during the preparation of your application. 4. Unless otherwise indicated, all sections of this form must be completed for the application to be formally received and assessed. -
Schumannella Luteola Gen. Nov., Sp. Nov., a Novel Genus of the Family Microbacteriaceae
J. Gen. Appl. Microbiol., 54, 253‒258 (2008) Full Paper Schumannella luteola gen. nov., sp. nov., a novel genus of the family Microbacteriaceae Sun-Young An*, Tian Xiao, and Akira Yokota Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113‒0032, Japan (Received February 28, 2008; Accepted June 24, 2008) An actinobacterial strain KHIAT, isolated from lichen in Tokyo, was taxonomically characterized using a polyphasic approach. The isolate is a Gram-positive, anaerobic, non-motile and rod- shaped bacterium. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolate is represented as an independent lineage distinctive from the Microbacteriaceae genera. The G+C content of DNA was 58.7 mol%. The chemotaxonomic characteristics of the isolate are cell wall peptidoglycan type (2,4-diaminobutyric acid), major cellular fatty acids (anteiso-C15:0 and iso-C16:0) and quinone type (MK-11 and MK-10). On the basis of the phenotypic and phyloge- netic distinctness, it is proposed that strain KHIAT represents a novel species in a new genus of the family Microbacteriaceae, Schumannella luteola gen. nov., sp. nov. The type strain is KHIAT (=JCM 23215T=TISTR 1824T). Key Words—Schumannella luteola gen. nov., sp. nov. Introduction butyric acid in the cell wall. Analyses of the 16S rRNA gene sequences from strain KHIAT showed that it was The family Microbacteriaceae currently contains 24 related to genera such as Leifsonia, Rhodoglobus, and genera, which are characterized by unsaturated major Salinibacterium of the family Microbacteriaceae. menaquinones (Collins and Jones, 1981) and B-type The aim of the present study is to elucidate the taxo- peptidoglycan (Park et al., 1993; Schleifer and Kan- nomic position of the isolate, using polyphasic taxon- dler, 1972; Stackebrandt et al., 1997). -
Systematic Research on Actinomycetes Selected According
Systematic Research on Actinomycetes Selected according to Biological Activities Dissertation Submitted in fulfillment of the requirements for the award of the Doctor (Ph.D.) degree of the Math.-Nat. Fakultät of the Christian-Albrechts-Universität in Kiel By MSci. - Biol. Yi Jiang Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany Supervised by Prof. Dr. Johannes F. Imhoff Kiel 2009 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: ______________________ Tag der mündlichen Prüfung: Kiel, ____________ Zum Druck genehmigt: Kiel, _____________ Summary Content Chapter 1 Introduction 1 Chapter 2 Habitats, Isolation and Identification 24 Chapter 3 Streptomyces hainanensis sp. nov., a new member of the genus Streptomyces 38 Chapter 4 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae 52 Chapter 5 A new member of the family Micromonosporaceae, Planosporangium flavogriseum gen nov., sp. nov. 67 Chapter 6 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea 87 Chapter 7 Discussion 99 Appendix a Resume, Publication list and Patent 115 Appendix b Medium list 122 Appendix c Abbreviations 126 Appendix d Poster (2007 VAAM, Germany) 127 Appendix e List of research strains 128 Acknowledgements 134 Erklärung 136 Summary Actinomycetes (Actinobacteria) are the group of bacteria producing most of the bioactive metabolites. Approx. 100 out of 150 antibiotics used in human therapy and agriculture are produced by actinomycetes. Finding novel leader compounds from actinomycetes is still one of the promising approaches to develop new pharmaceuticals. The aim of this study was to find new species and genera of actinomycetes as the basis for the discovery of new leader compounds for pharmaceuticals. -
Of Bergey's Manual
BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Five The Actinobacteria, Part A and B BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Five The Actinobacteria, Part A and B Michael Goodfellow, Peter Kämpfer, Hans-Jürgen Busse, Martha E. Trujillo, Ken-ichiro Suzuki, Wolfgang Ludwig and William B. Whitman EDITORS, VOLUME FIVE William B. Whitman DIRECTOR OF THE EDITORIAL OFFICE Aidan C. Parte MANAGING EDITOR EDITORIAL BOARD Fred A. Rainey, Chairman, Peter Kämpfer, Vice Chairman, Paul De Vos, Jongsik Chun, Martha E. Trujillo and William B. Whitman WITH CONTRIBUTIONS FROM 116 COLLEAGUES William B. Whitman Bergey’s Manual Trust Department of Microbiology 527 Biological Sciences Building University of Georgia Athens, GA 30602-2605 USA ISBN 978-0-387-95043-3 ISBN 978-0-387-68233-4 (eBook) DOI 10.1007/978-0-387-68233-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012930836 © 2012, 1984–1989 Bergey’s Manual Trust Bergey’s Manual is a registered trademark of Bergey’s Manual Trust. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. -
Actinobacteria Structure in Autogenic, Hydrogenic and Lithogenic Cultivated and Non-Cultivated Soils: a Culture-Independent Approach
agronomy Article Actinobacteria Structure in Autogenic, Hydrogenic and Lithogenic Cultivated and Non-Cultivated Soils: A Culture-Independent Approach Agnieszka Woli ´nska 1,* , Dorota Górniak 2, Urszula Zielenkiewicz 3 , Agnieszka Ku´zniar 1, Dariusz Izak 3 , Artur Banach 1 and Mieczysław Błaszczyk 4 1 Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin; Konstantynów St. 1 I, 20-708 Lublin, Poland; [email protected] (A.K.); [email protected] (A.B.) 2 Department of Microbiology and Mycology, University of Warmia and Mazury in Olsztyn; Oczapowskiego St. 1a, 10-719 Olsztyn, Poland; [email protected] 3 Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS; Pawi´nskiegoSt. 5a, 02-206 Warsaw, Poland; [email protected] (U.Z.); [email protected] (D.I.) 4 Department of Microbial Biology, Warsaw University of Life Sciences; Nowoursynowska 159/37 St., 02-776 Warsaw, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-81-454-54-60; Fax: +48-81-445-46-11 Received: 12 August 2019; Accepted: 27 September 2019; Published: 29 September 2019 Abstract: The aim of the study was to determine the Actinobacteria structure in cultivated (C) versus non-cultivated (NC) soils divided into three groups (autogenic, hydrogenic, lithogenic) with consideration its formation process in order to assess the Actinobacteria sensitivity to agricultural soil use and soil genesis and to identify factors affecting their abundance. Sixteen C soil samples and sixteen NC samples serving as controls were taken for the study. Next generation sequencing (NGS) of the 16S rRNA metagenomic amplicons (Ion Torrent™ technology) and Denaturing Gradient Gel Electrophoresis (DGGE) were applied for precise determination of biodiversity.