DOCSLIB.ORG

Appendix 1. Validly Published Names, Conserved and Rejected Names, And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al. et al. (2005vi) (2005xxii) Chromatiales Imhoff 2005, 2235VP – Valid publication: Validation Caldilineae Yamada et al. 2006, 1339VP List no. 106 – Effective publication: Imhoff (2005) Deltaproteobacteria Kuever et al. 2006, 1VP – Valid publication: Desulfarculales corrig. Kuever et al. 2006, 1VP – Valid publica- Validation List no. 107 – Effective publication: Kuever et al. tion: Validation List no. 107 – Effective publication: Kuever (2005a) et al. (2005o) Epsilonproteobacteria Garrity et al. 2006, 2VP – Valid publication: Desulfobacterales Kuever et al. 2006, 2VP – Valid publication: Valida- Validation List no. 107 – Effective publication: Garrity et al. tion List no. 107 – Effective publication: Kuever et al. (2005j) (2005xxxviii) Desulfovibrionales Kuever et al. 2006, 2VP – Valid publication: Gammaproteobacteria Garrity et al. 2005, 2236VP – Valid publica- Validation List no. 107 – Effective publication: Kuever et al. tion: Validation List no. 106 – Effective publication: Garrity (2005d) et al. (2005ii) Desulfurellales Kuever et al. 2006, 2VP – Valid publication: Valida- Ktedonobacteria corrig. Cavaletti et al. 2007, 433VP – Valid publi- tion List no. 107 – Effective publication: Kuever et al. (2005b) cation: Validation List no. 114 – Effective publication: Caval- Desulfuromonadales corrig. Kuever et al. 2006, 2VP – Valid publica- etti et al. (2006b) tion: Validation List no. 107 – Effective publication: Kuever Thermolithobacteria Sokolova et al. 2007, 1372VP – Valid publica- et al. (2005r) tion: Validation List no. 116 – Effective publication: Sokolova Hydrogenophilales Garrity et al. 2006, 2VP – Valid publication: et al. (2007) Validation List no. 107 – Effective publication: Garrity et al. Opitutae Choo et al. 2007, 535VP (2005xxvi) New orders Kordiimonadales K.K. Kwon et al. 2005, 2036VP VP Acidithiobacillales Garrity et al. 2005, 2235VP – Valid publica- Ktedonobacterales corrig. Cavaletti et al. 2007, 433 – Valid pub- tion: Validation List no. 106 – Effective publication: Garrity lication: Validation List no. 114 – Effective publication: Cav- et al. (2005iii) aletti et al. (2006b) VP Aeromonadales Martin-Carnahan and Joseph 2005, 2235VP – Valid Legionellales Garrity et al. 2005, 2236 – Valid publication: Valida- publication: Validation List no. 106 – Effective publication: tion List no. 106 – Effective publication: Garrity et al. (2005ix) Martin-Carnahan and Joseph (2005) Lentisphaerales Cho et al. 2004, 1005VP – Valid publication: Valida- tion List no. 98 – Effective publication: J.C. Cho et al. (2004) Methylococcales Bowman 2005, 2236VP – Valid publication: Valida- tion List no. 106 – Effective publication: Bowman (2005b) * Citations for the original authorities for basonyms, synonyms, and emendations Methylophilales Garrity et al. 2006, 2VP – Valid publication: Vali- do not appear in the bibliography unless cited elsewhere in this book. References for Validation Lists and Lists of Changes in Taxonomic Opinion are provided at dation List no. 107 – Effective publication: Garrity et al. the end of the chapter. (2005xxviii) 1319 1320 APPENDIX 1 Natranaerobiales Mesbah et al. 2007, 2511VP New families Nautiliales Miroshnichenko et al. 2004, 43VP Acidithiobacillaceae Garrity et al. 2005, 2235VP – Valid publication: Val- Neisseriales Tønjum 2006, 2VP – Valid publication: Validation List idation List no. 106 – Effective publication: Garrity et al. (2005iv) no. 107 – Effective publication: Tønjum (2005) Actinospicaceae Cavaletti et al. 2006a, 1751VP Nitrosomonadales Garrity et al. 2006, 2VP – Valid publication: Alcanivoracaceae corrig. Golyshin et al. 2005, 2235VP – Valid pub- Validation List no. 107 – Effective publication: Garrity et al. lication: Validation List no. 106 – Effective publication: Goly- (2005xxx) shin et al. (2005) Oceanospirillales Garrity et al. 2005, 2236VP – Valid publica- Anaerolineaceae Yamada et al. 2006, 1338VP tion: Validation List no. 106 – Effective publication: Garrity Bacteriovoracaceae Davidov and Jurkevitch 2004, 1450VP et al. (2005xi) Bdellovibrionaceae Garrity et al. 2006, 1VP – Valid publication: Opitutales Choo et al. 2007, 536VP Validation List no. 107 – Effective publication: Garrity et al. Pasteurellales Garrity et al. 2005, 2236VP – Valid publication: (2005xxxvii) Validation List no. 106 – Effective publication: Garrity et al. According to Rule 51b(1), the family name Bdellovibrionaceae (2005xiv) Garrity et al. 2006 is illegitimate. Puniceicoccales Choo et al. 2007, 536VP Beijerinckiaceae Garrity et al. 2006, 1VP – Valid publication: Vali- Rhizobiales Kuykendall 2006, 3VP – Valid publication: Validation dation List no. 107 – Effective publication: Garrity et al. List no. 107 – Effective publication: Kuykendall (2005) (2005xviii) According to Rule 51b(1), the order name Rhizobiales Kuyk- Bradyrhizobiaceae Garrity et al. 2006, 1VP – Valid publication: endall 2006 is illegitimate. Validation List no. 107 – Effective publication: Garrity et al. Rhodobacterales Garrity et al. 2006, 3VP – Valid publication: Vali- (2005xix) dation List no. 107 – Effective publication: Garrity et al. According to Rule 51b(1), the family name Bradyrhizobiaceae (2005xvi) Garrity et al. 2006 is illegitimate. Rhodocyclales Garrity et al. 2006, 3VP – Valid publication: Vali- Burkholderiaceae Garrity et al. 2006, 1VP – Valid publication: dation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xxxii) (2005xxiv) Sphingomonadales Yabuuchi and Kosako 2006, 3VP – Valid publica- Caldilineaceae Yamada et al. 2006, 1339VP tion: Validation List no. 107 – Effective publication: Yabuuchi Catenulisporaceae Busti et al. 2006, 1745VP and Kosako (2005) Colwelliaceae Ivanova et al. 2004d, 1785VP Syntrophobacterales Kuever et al. 2006, 3VP – Valid publication: VP Validation List no. 107 – Effective publication: Kuever et al. Conexibacteraceae Stackebrandt 2005, 547 – Valid publication: (2005t) Validation List no. 102 – Effective publication: Stackebrandt (2004) Thermolithobacterales Sokolova et al. 2007, 1372VP – Valid publica- VP tion: Validation List no. 116 – Effective publication: Sokolova Coxiellaceae Garrity et al. 2005, 2235 – Valid publication: Val- et al. (2007) idation List no. 106 – Effective publication: Garrity et al. (2005x) Thiotrichales Garrity et al. 2005, 2236VP – Valid publication: VP Validation List no. 106 – Effective publication: Garrity et al. Desulfarculaceae Kuever et al. 2006, 1 – Valid publication: (2005vii) Validation List no. 107 – Effective publication: Kuever et al. (2005p) Victivallales Cho et al. 2004, 1005VP – Valid publication: Valida- VP tion List no. 98 – Effective publication: J.C. Cho et al. (2004) Desulfobacteraceae Kuever et al. 2006, 2 – Valid publication: Validation List no. 107 – Effective publication: Kuever et al. Xanthomonadales Saddler and Bradbury 2005, 2236VP – Valid (2005k) publication: Validation List no. 106 – Effective publication: VP Saddler and Bradbury (2005a) Desulfobulbaceae Kuever et al. 2006, 2 – Valid publication: Valida- tion List no. 107 – Effective publication: Kuever et al. (2005n) New suborders Desulfohalobiaceae Kuever et al. 2006, 2VP – Valid publication: Catenulisporineae Cavaletti et al. 2006a, 1751VP Validation List no. 107 – Effective publication: Kuever et al. Cystobacterineae Reichenbach 2007, 894VP – Valid publication: (2005g) Validation List no. 115 – Effective publication: Reichenbach Desulfomicrobiaceae Kuever et al. 2006, 2VP – Valid publication: Vali- (2005a) dation List no. 107 – Effective publication: Kuever et al. (2005f) Nannocystineae Reichenbach 2007, 894VP – Valid publication: Desulfonatronaceae corrig. Kuever et al. 2006, 2VP – Valid publica- Validation List no.
Recommended publications
  • The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil

    The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil

    THE ROLE OF EARTHWORM GUT-ASSOCIATED MICROORGANISMS IN THE FATE OF PRIONS IN SOIL Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Taras Jur’evič Nechitaylo aus Krasnodar, Russland 2 Acknowledgement I would like to thank Prof. Dr. Kenneth N. Timmis for his guidance in the work and help. I thank Peter N. Golyshin for patience and strong support on this way. Many thanks to my other colleagues, which also taught me and made the life in the lab and studies easy: Manuel Ferrer, Alex Neef, Angelika Arnscheidt, Olga Golyshina, Tanja Chernikova, Christoph Gertler, Agnes Waliczek, Britta Scheithauer, Julia Sabirova, Oleg Kotsurbenko, and other wonderful labmates. I am also grateful to Michail Yakimov and Vitor Martins dos Santos for useful discussions and suggestions. I am very obliged to my family: my parents and my brother, my parents on low and of course to my wife, which made all of their best to support me. 3 Summary.....................................................………………………………………………... 5 1. Introduction...........................................................................................................……... 7 Prion diseases: early hypotheses...………...………………..........…......…......……….. 7 The basics of the prion concept………………………………………………….……... 8 Putative prion dissemination pathways………………………………………….……... 10 Earthworms: a putative factor of the dissemination of TSE infectivity in soil?.………. 11 Objectives of the study…………………………………………………………………. 16 2. Materials and Methods.............................…......................................................……….. 17 2.1 Sampling and general experimental design..................................................………. 17 2.2 Fluorescence in situ Hybridization (FISH)………..……………………….………. 18 2.2.1 FISH with soil, intestine, and casts samples…………………………….……... 18 Isolation of cells from environmental samples…………………………….……….
  • Content Dental Care

    Content Dental Care

    DENTAL Care Content Dental Care 134 How must the professional proceed in order to obtain reimbursement for dental care? 137 Why is the professional/provider asking the client to pay for their service? 138 Reason 1 - The professional/provider refuses to collaborate with Health Canada to receive payment for the services or the professional is unfamiliar with Heath Canada’s reimbursement process. 140 Reason 2 - The client did not indicate their First Nations status to the professional/provider. 141 Reason 3 - Difference in cost between the amount reimbursed by Health Canada and the amount being billed by the professional/provider. 143 Reason 4 - Non-respect for the frequency limits in the client’s file (e.g. not enough time has passed between two treatments). 144 Reason 5 - The dental care being requested is excluded from the program. 145 Frequently Asked Questions DENTAL CARE Since February 2013, preauthorisation for Health Canada’s dental care services is performed by the National Dental Predetermination Centre located in Ottawa. Health Canada’s Dental Care program covers care and services when these are not covered by Quebec’s health insurance plan. Client eligibility is described in the following table. ELIGIBLE CLIENTELE RAMQ NIHB • Children nine years of age or under (ex- • The costs for cleaning, periodontal scaling cludes: cleaning, periodontal scaling and and the application of fluoride and sealants fluoride) for children ages nine years or under • Provincial income security recipients • First Nations members ten years and up (on- and off-reserve) See the Provincial Health Care and • Income security recipients on-reserve Services section The services covered by Health Canada are described in: • The Dental Benefits Guide (appended); • The NIHB information booklet, pages 8 to 14.
  • Tessaracoccus Arenae Sp. Nov., Isolated from Sea Sand

    Tessaracoccus Arenae Sp. Nov., Isolated from Sea Sand

    TAXONOMIC DESCRIPTION Thongphrom et al., Int J Syst Evol Microbiol 2017;67:2008–2013 DOI 10.1099/ijsem.0.001907 Tessaracoccus arenae sp. nov., isolated from sea sand Chutimon Thongphrom,1 Jong-Hwa Kim,1 Nagamani Bora2,* and Wonyong Kim1,* Abstract A Gram-stain positive, non-spore-forming, non-motile, facultatively anaerobic bacterial strain, designated CAU 1319T, was isolated from sea sand and the strain’s taxonomic position was investigated using a polyphasic approach. Strain CAU 1319T grew optimally at 30 C and at pH 7.5 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain CAU 1319T belongs to the genus Tessaracoccus, and is closely related to Tessaracoccus lapidicaptus IPBSL-7T (similarity 97.69 %), Tessaracoccus bendigoensis Ben 106T (similarity 95.64 %) and Tessaracoccus T T flavescens SST-39 (similarity 95.84 %). Strain CAU 1319 had LL-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-9 (H4) as the predominant menaquinone, and anteiso-C15 : 0 as the major fatty acid. The polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, two unidentified aminolipids, three unidentified phospholipids and one unidentified glycolipid. Predominant polyamines were spermine and spermidine. The DNA–DNA hybridization value between strain CAU 1319T and T. lapidicaptus IPBSL-7T was 24 %±0.2. The DNA G+C content of the novel strain was 69.5 mol %. On the basis of phenotypic and chemotaxonomic properties, as well as phylogenetic relatedness, strain CAU 1319Tshould be classified as a novel species of the genus Tessaracoccus, for which the name Tessaracoccus arenae sp.
  • Updating the Taxonomic Toolbox: Classification of Alteromonas Spp

    Updating the Taxonomic Toolbox: Classification of Alteromonas Spp

    1 Updating the taxonomic toolbox: classification of Alteromonas spp. 2 using Multilocus Phylogenetic Analysis and MALDI-TOF Mass 3 Spectrometry a a a 4 Hooi Jun Ng , Hayden K. Webb , Russell J. Crawford , François a b b c 5 Malherbe , Henry Butt , Rachel Knight , Valery V. Mikhailov and a, 6 Elena P. Ivanova * 7 aFaculty of Life and Social Sciences, Swinburne University of Technology, 8 PO Box 218, Hawthorn, Vic 3122, Australia 9 bBioscreen, Bio21 Institute, The University of Melbourne, Vic 3010, Australia 10 cG.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian 11 Academy of Sciences, Vladivostok 690022, Russian Federation 12 13 *Corresponding author: Tel: +61-3-9214-5137. Fax: +61-3-9214-5050. 14 E-mail: [email protected] 15 16 Abstract 17 Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, 18 heterotrophic marine bacteria, known for their versatile metabolic activities. 19 Identification and classification of novel species belonging to the genus Alteromonas 20 generally involves DNA-DNA hybridization (DDH) as distinct species often fail to be 1 21 resolved at the 97% threshold value of the 16S rRNA gene sequence similarity. In this 22 study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix- 23 Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF 24 MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic 25 analysis incorporating five house-keeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) 26 revealed a threshold value of 98.9% that could be considered as the species cut-off 27 value for the delineation of Alteromonas spp.
  • Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT

    Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT

    bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 2019. 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 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity.
  • UNIVERSITY of CALIFORNIA, SAN DIEGO Indicators of Iron

    UNIVERSITY of CALIFORNIA, SAN DIEGO Indicators of Iron

    UNIVERSITY OF CALIFORNIA, SAN DIEGO Indicators of Iron Metabolism in Marine Microbial Genomes and Ecosystems A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Shane Lahman Hogle Committee in charge: Katherine Barbeau, Chair Eric Allen Bianca Brahamsha Christopher Dupont Brian Palenik Kit Pogliano 2016 Copyright Shane Lahman Hogle, 2016 All rights reserved . The Dissertation of Shane Lahman Hogle is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2016 iii DEDICATION Mom, Dad, Joel, and Marie thank you for everything iv TABLE OF CONTENTS Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents .................................................................................................................v List of Figures ................................................................................................................... vii List of Tables ..................................................................................................................... ix Acknowledgements ..............................................................................................................x Vita ..................................................................................................................................
  • Tessaracoccus Massiliensis Sp. Nov., a New Bacterial Species Isolated from the Human Gut

    Tessaracoccus Massiliensis Sp. Nov., a New Bacterial Species Isolated from the Human Gut

    TAXONOGENOMICS: GENOME OF A NEW ORGANISM Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut E. Seck1, S. I. Traore1, S. Khelaifia1, M. Beye1, C. Michelle1, C. Couderc1, S. Brah2, P.-E. Fournier1, D. Raoult1,3 and G. Dubourg1 1) Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France, 2) Hôpital National de Niamey, Niamey, Niger and 3) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7T (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes. © 2016 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: culturomics, genome, human gut, taxono-genomics, Tessaracoccus massiliensis Original Submission: 23 February 2016; Revised Submission: 28 April 2016; Accepted: 3 May 2016 Article published online: 28 May 2016 development of new tools for the sequencing of DNA [5],we Corresponding author: G. Dubourg, Aix-Marseille Université, introduced a new way of describing the novel bacterial species URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, [6]. This includes, among other features, their genomic [7–11] France and proteomic information obtained by matrix-assisted laser E-mail: [email protected] desorption-ionization time-of-flight (MALDI-TOF-MS) analysis [12].
  • Community Structure Analysis �9

    Community Structure Analysis 9

    Biodegradation of Polystyrene Foam by the Microorganisms from Landfill Pat Pataranutaporn ! Assistant prof. Savaporn Supaphol prof. Amornrat Phongdara Sureeporn Nualkaew Hi, I would like to invite you to take a look on my research Pat Introduction !3 “Styrofoam” Polystyrene Disadvantage Physical Properties ! • chemical formula is (C8H8)n • Non-biodegradable in the environment • monomer styrene • Made from non-renewable petroleum products • Thermoplastic • Chronic, low-level exposure risks undetermined • blowing agents Introduction !4 Bacteria nutritional requirements ! ‣ Energy source Biodegradation ‣ Carbon source Possibly work? ‣ Nitrogen source ‣ Minerals ‣ Water ‣ Growth factors Polystyrene structure http://faculty.ccbcmd.edu/courses/bio141/ lecguide/unit6/metabolism/growth/factors.html Introduction !5 Aims of the research ‣To identify the microbe that able to growth in the condition that polystyrene is a sole carbon source ! ‣To study the changing of microbe community structure in the selective culture which polystyrene is a sole carbon source ! ‣To observe the biodegradability of polystyrene To analyse the by product of polystyrene after degradation Methodology Methodology !7 Agar cultivation Community fingerprint 2 16s Ribosomal RNA Microbe Screening months later identification sampling Cultivation Molecular cloning Phylogenetic tree Degradability observation (SEM) Methodology Microbe sampling & cultivation !8 Agar cultivation Community fingerprint 2 16s Ribosomal RNA Microbe Screening months later identification sampling Cultivation
  • Metal Transformation by a Novel Pelosinus Isolate from a Subsurface Environment

    Metal Transformation by a Novel Pelosinus Isolate from a Subsurface Environment

    INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 The INL is a U.S. Department of Energy National Laboratory operated by Battelle Energy Alliance INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 Idaho National Laboratory Idaho Falls, Idaho 83415 http://www.inl.gov Prepared for the U.S. Department of Energy Office of Nuclear Energy Under DOE Idaho Operations Office Contract DE-AC07-05ID14517 fmicb-09-01689 July 25, 2018 Time: 20:42 # 1 ORIGINAL RESEARCH published: xx July 2018 doi: 10.3389/fmicb.2018.01689 1 58 2 59 3 60 4 61 5 62 6 63 7 64 8 65 9 Metal Transformation by a Novel 66 10 67 11 Pelosinus Isolate From a Subsurface 68 12 69 13 Environment 70 14 71 15 Allison E. Ray1,2, Stephanie A. Connon1,3, Andrew L. Neal4†, Yoshiko Fujita2, 72 5 2† 1 16 David E. Cummings , Jani C. Ingram and Timothy S. Magnuson * 73 17 74 1 Department of Biological Sciences, Idaho State University, Pocatello, ID, United States, 2 Bioenergy Technologies, Idaho 18 3 75 Edited by: National Laboratory, Idaho Falls, ID, United States, California Institute of Technology, Pasadena, CA, United States, 19 4 5 76 Pankaj Kumar Arora, Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States, Department of Biology, Point Loma 20 77 Babasaheb Bhimrao Ambedkar Nazarene University, San Diego, CA, United States 21 University, India 78 22 79 Reviewed by: The capability of microorganisms to alter metal speciation offers potential for 23 80 Ramprasad E.V.V., the development of new strategies for immobilization of toxic metals in the 24 University of Hyderabad, India 81 25 Bärbel Ulrike Fösel, environment.
  • Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain

    Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain

    Lawrence Berkeley National Laboratory Recent Work Title RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Permalink https://escholarship.org/uc/item/9f26h2cp Journal Applied and environmental microbiology, 83(14) ISSN 0099-2240 Authors Yu, Dianzhen Xia, Ming Zhang, Liping et al. Publication Date 2017-07-01 DOI 10.1128/aem.00709-17 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RpoN (σσ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain Dianzhen Yu,a,b Ming Xia,a,b Liping Zhang,a Yulong Song,a You Duan,a,b Tong Yuan,d,f Minjie Yao,c Liyou Wu,d Chunyuan Tian,e Zhenbin Wu,a Xiangzhen Li,c Jizhong Zhou,d Dongru Qiua Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Chinaa ; University of Chinese Academy of Sciences, Beijing, Chinab; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Chinac ; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USAd; School of Life Sciences and Technology, Hubei Engineering University, Xiaogan, Chinae; College of Life Science, Henan Agricultural University, Zhengzhou, Chinaf ABSTRACT Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincola tertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation.
  • Azonexus Hydrophilus Sp. Nov., a Nifh Gene-Harbouring Bacterium Isolated from Freshwater

    Azonexus Hydrophilus Sp. Nov., a Nifh Gene-Harbouring Bacterium Isolated from Freshwater

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by National Chung Hsing University Institutional Repository International Journal of Systematic and Evolutionary Microbiology (2008), 58, 946–951 DOI 10.1099/ijs.0.65434-0 Azonexus hydrophilus sp. nov., a nifH gene-harbouring bacterium isolated from freshwater Jui-Hsing Chou,1 Sing-Rong Jiang,2 Jang-Cheon Cho,3 Jaeho Song,3 Mei-Chun Lin2 and Wen-Ming Chen2 Correspondence 1Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, Wen-Ming Chen National Chung Hsing University, Taichung, Taiwan [email protected] 2Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan 3Division of Biology and Ocean Sciences, Inha University, Yonghyun Dong, Incheon 402-751, Republic of Korea Three Gram-negative, non-pigmented, rod-shaped, facultatively aerobic bacterial strains, designated d8-1T, d8-2 and IMCC1716, were isolated from a freshwater spring sample and a eutrophic freshwater pond. Based on characterization using a polyphasic approach, the three strains showed highly similar phenotypic, physiological and genetic characteristics. All of the strains harboured the nitrogenase gene nifH, but nitrogen-fixing activities could not be detected in nitrogen-free culture media. The three strains shared 99.6–99.7 % 16S rRNA gene sequence similarity and showed 89–100 % DNA–DNA relatedness, suggesting that they represent a single genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains d8-1T, d8-2 and IMCC1716 formed a monophyletic branch in the periphery of the evolutionary radiation occupied by the genus Azonexus.
  • Rapport Nederlands

    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.