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Hwang C, Copeland A, Lucas S, Lapidus A, Barry K, Detter JC, Glavina Del Rio T, Hammon N, Israni S, Dalin E, Tice H, Pitluck S, Chertkov O, Brettin T, Bruce D, Han C, Schmutz J, Larimer F, Land ML, Hauser L, Kyrpides N, Mikhailova N, Ye Q, Zhou J, Richardson P, Fields MW. Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds. Genome Announc 2016; 4:e01226-16. [PMID: 27811105 PMCID: PMC5095475 DOI: 10.1128/genomea.01226-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 11/20/2022]
Abstract
Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.
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Affiliation(s)
- C Hwang
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - A Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - S Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - A Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - K Barry
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - J C Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - N Hammon
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - S Israni
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - E Dalin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - H Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - S Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - O Chertkov
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - T Brettin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - D Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - C Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - J Schmutz
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - F Larimer
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - M L Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - L Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - N Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - N Mikhailova
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Q Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - J Zhou
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma, USA
| | - P Richardson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - M W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
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2
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Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NC. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Stand Genomic Sci 2016; 11:70. [PMID: 27617060 PMCID: PMC5018182 DOI: 10.1186/s40793-016-0194-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/03/2016] [Indexed: 01/26/2023] Open
Abstract
Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
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Affiliation(s)
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David C Bruce
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David Sims
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Thomas S Brettin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - John C Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Cliff S Han
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Frank Larimer
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | | | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052 Australia
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Carl R Woese
- B103 Chemical and Life Sciences Laboratory, University of Illinois at Urbana-Champaign, MC-110, 601 South Goodwin Avenue, Urbana, IL 61801 USA
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3
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Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci 2014; 9:10. [PMID: 25780503 PMCID: PMC4334474 DOI: 10.1186/1944-3277-9-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/21/2022] Open
Abstract
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
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Affiliation(s)
- Carmen Scheuner
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Brian J Tindall
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cynthia D Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Romano Mwirichia
- Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Birte Abt
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - John C Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Markus Göker
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
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4
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Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, MA J, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki KI, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014; 12:e1001920. [PMID: 25093819 PMCID: PMC4122341 DOI: 10.1371/journal.pbio.1001920] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This manuscript calls for an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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Affiliation(s)
- Nikos C. Kyrpides
- DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (NCK); (HPK)
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics Research, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jonathan A. Eisen
- University of California, Davis, Davis, California, United States of America
| | - Tanja Woyke
- DOE-Joint Genome Institute, Walnut Creek, California, United States of America
| | - Markus Göker
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Brian J. Beck
- American Type Culture Collection (ATCC), Manassas, Virginia, United States of America
| | - Patrick S. G. Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America
| | - Jongsik Chun
- School of Biological Sciences and Chunlab Inc., Seoul National University, Seoul, Korea
| | - Rita R. Colwell
- University of Maryland, College Park, College Park, Maryland, United States of America
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - Peter Dawyndt
- Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium
| | - Tom Dedeurwaerdere
- Centre for Philosophy of Law, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Edward F. DeLong
- Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America
| | - Paul De Vos
- Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium
- Ghent University, BCCM/LMG Bacteria collection, Laboratory of Microbiology, Ghent, Belgium
| | - Timothy J. Donohue
- University of Wisconsin-Madison, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
| | - Xiu-Zhu Dong
- Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China
| | - Dusko S. Ehrlich
- Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Claire Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jack Gilbert
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Paul Gilna
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | - Janet K. Jansson
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jay D. Keasling
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute (JBEI), Berkeley, California, United States of America
| | - Rob Knight
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | - David Labeda
- ARS, USDA, National Center for Agricultural Utilization Research, Peoria, Illinois, United States of America
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, Korea
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, Kunming, People's Republic of China
| | - Juncai MA
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Victor Markowitz
- DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Edward R. B. Moore
- CCUG - Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Mark Morrison
- Diamantina Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Folker Meyer
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Karen E. Nelson
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Moriya Ohkuma
- Riken Bioresource Center, Japan Collection of Microorganisms, Hirosawa, Wako, Saitama, Japan
| | - Christos A. Ouzounis
- Chemical Process & Energy Resources Institute, Centre for Research & Technology, Thessalonica, Greece
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Norman Pace
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Julian Parkhill
- The Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nan Qin
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ramon Rossello-Mora
- Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Illes Balears, Spain
| | - Johannes Sikorski
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - David Smith
- CABI, Bakeham Lane, Egham, Surrey, United Kingdom
| | - Mitch Sogin
- Josephine Bay Paul Center for Comparative Evolution and Molecular Biology, MBL, Woods Hole, Massachusetts, United States of America
| | - Rick Stevens
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Uli Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | | | - Dorothea Taylor
- NamesforLife, LLC, East Lansing, Michigan, United States of America
| | - Jim M. Tiedje
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Brian Tindall
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Wagner
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
| | - George Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jean Weissenbach
- Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, France
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jun Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lixin Zhang
- Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Dawn Field
- U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, Oxford, United Kingdom
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - George M. Garrity
- NamesforLife, LLC, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Hans-Peter Klenk
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- * E-mail: (NCK); (HPK)
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5
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Göker M, Spring S, Scheuner C, Anderson I, Zeytun A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci 2014; 9:1105-17. [PMID: 25197486 PMCID: PMC4148951 DOI: 10.4056/sigs.3016383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Ahmet Zeytun
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Yun-Juan Chang
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Cynthia D Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - John C Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA ; University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
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6
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Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci 2014; 9:687-703. [PMID: 25197454 PMCID: PMC4148953 DOI: 10.4056/sigs.3828824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
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Affiliation(s)
- Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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7
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Göker M, Lu M, Fiebig A, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Mayilraj S, Rohde M, Detter JC, Bunk B, Spring S, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci 2014; 9:1076-88. [PMID: 25197484 PMCID: PMC4149034 DOI: 10.4056/sigs.5138968] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pre-genome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and annotation of the type strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia of B acteria and Archaea project.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shanmugam Mayilraj
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Boyke Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Reinhard Wirth
- University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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8
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Dover N, Barash JR, Burke JN, Hill KK, Detter JC, Arnon SS. Arrangement of the Clostridium baratii F7 toxin gene cluster with identification of a σ factor that recognizes the botulinum toxin gene cluster promoters. PLoS One 2014; 9:e97983. [PMID: 24853378 PMCID: PMC4031146 DOI: 10.1371/journal.pone.0097983] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 04/27/2014] [Indexed: 12/14/2022] Open
Abstract
Botulinum neurotoxin (BoNT) is the most poisonous substances known and its eight toxin types (A to H) are distinguished by the inability of polyclonal antibodies that neutralize one toxin type to neutralize any of the other seven toxin types. Infant botulism, an intestinal toxemia orphan disease, is the most common form of human botulism in the United States. It results from swallowed spores of Clostridium botulinum (or rarely, neurotoxigenic Clostridium butyricum or Clostridium baratii) that germinate and temporarily colonize the lumen of the large intestine, where, as vegetative cells, they produce botulinum toxin. Botulinum neurotoxin is encoded by the bont gene that is part of a toxin gene cluster that includes several accessory genes. We sequenced for the first time the complete botulinum neurotoxin gene cluster of nonproteolytic C. baratii type F7. Like the type E and the nonproteolytic type F6 botulinum toxin gene clusters, the C. baratii type F7 had an orfX toxin gene cluster that lacked the regulatory botR gene which is found in proteolytic C. botulinum strains and codes for an alternative σ factor. In the absence of botR, we identified a putative alternative regulatory gene located upstream of the C. baratii type F7 toxin gene cluster. This putative regulatory gene codes for a predicted σ factor that contains DNA-binding-domain homologues to the DNA-binding domains both of BotR and of other members of the TcdR-related group 5 of the σ70 family that are involved in the regulation of toxin gene expression in clostridia. We showed that this TcdR-related protein in association with RNA polymerase core enzyme specifically binds to the C. baratii type F7 botulinum toxin gene cluster promoters. This TcdR-related protein may therefore be involved in regulating the expression of the genes of the botulinum toxin gene cluster in neurotoxigenic C. baratii.
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Affiliation(s)
- Nir Dover
- Infant Botulism Treatment and Prevention Program, California Department of Public Health, Richmond, California, United States of America
| | - Jason R. Barash
- Infant Botulism Treatment and Prevention Program, California Department of Public Health, Richmond, California, United States of America
| | - Julianne N. Burke
- Infant Botulism Treatment and Prevention Program, California Department of Public Health, Richmond, California, United States of America
| | - Karen K. Hill
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - John C. Detter
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Stephen S. Arnon
- Infant Botulism Treatment and Prevention Program, California Department of Public Health, Richmond, California, United States of America
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9
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Dogs M, Voget S, Teshima H, Petersen J, Davenport K, Dalingault H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Standfest S, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Klenk HP, Göker M, Brinkhoff T. Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci 2013; 9:334-50. [PMID: 24976890 PMCID: PMC4062626 DOI: 10.4056/sigs.4448212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sonja Standfest
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
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10
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Galardini M, Bazzicalupo M, Biondi E, Brambilla E, Brilli M, Bruce D, Chain P, Chen A, Daligault H, Davenport KW, Deshpande S, Detter JC, Goodwin LA, Han C, Han J, Huntemann M, Ivanova N, Klenk HP, Kyrpides NC, Markowitz V, Mavrommatis K, Mocali S, Nolan M, Pagani I, Pati A, Pini F, Pitluck S, Spini G, Szeto E, Teshima H, Woyke T, Mengoni A. Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58. Stand Genomic Sci 2013; 9:325-33. [PMID: 24976889 PMCID: PMC4062632 DOI: 10.4056/sigs.3797438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Ensifer (syn. Sinorhizobium) meliloti is an important symbiotic bacterial species that fixes nitrogen. Strains BO21CC and AK58 were previously investigated for their substrate utilization and their plant-growth promoting abilities showing interesting features. Here, we describe the complete genome sequence and annotation of these strains. BO21CC and AK58 genomes are 6,985,065 and 6,974,333 bp long with 6,746 and 6,992 genes predicted, respectively.
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Affiliation(s)
- Marco Galardini
- Department of Biology, University of Firenze, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Department of Biology, University of Firenze, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Italy
| | - Emanuele Biondi
- Interdisciplinary Research Institute - CNRS, Villenenuve d'Ascq, France
| | - Eveline Brambilla
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matteo Brilli
- Edmund Mach Foundation, San Michele all'Adige, Italy
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hajnalka Daligault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | | | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | | | | | - Stefano Mocali
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Centro di Ricerca per l'Agropedologia e la Pedologia, Firenze, Italy
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Francesco Pini
- Interdisciplinary Research Institute - CNRS, Villenenuve d'Ascq, France
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Giulia Spini
- Department of Biology, University of Firenze, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Italy
| | - Ernest Szeto
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alessio Mengoni
- Department of Biology, University of Firenze, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Italy
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11
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Meier-Kolthoff JP, Lu M, Huntemann M, Lucas S, Lapidus A, Copeland A, Pitluck S, Goodwin LA, Han C, Tapia R, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Woyke T, Kyrpides NC, Klenk HP. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)). Stand Genomic Sci 2013; 9:28-41. [PMID: 24501643 PMCID: PMC3910552 DOI: 10.4056/sigs.4207886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
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Affiliation(s)
- Jan P Meier-Kolthoff
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Megan Lu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St.Petersburg, Russia
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Gabriele Pötter
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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12
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Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Rohde M, Mayilraj S, Spring S, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. Stand Genomic Sci 2013; 9:57-70. [PMID: 24501645 PMCID: PMC3910556 DOI: 10.4056/sigs.4237901] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883(T), the type strain of T. acidaminovorans, stain Z-9701(T) is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
| | - Jan P. Meier-Kolthoff
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hazuki Teshima
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shanmugam Mayilraj
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
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13
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Anderson I, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Lang E, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a xanthomonade isolated from Lilium auratium Lindl. Stand Genomic Sci 2013; 9:83-92. [PMID: 24501647 PMCID: PMC3910546 DOI: 10.4056/sigs.4338002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67(T) was initially (1958) identified as a member of 'Acetobacter aurantius', a name that was not considered for the approved list. Kondô 67(T) was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia . The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67(T) is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Huzuki Teshima
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St.Petersburg, Russia
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Elke Lang
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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14
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Buddruhs N, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Gronow S, Kyrpides NC, Woyke T, Göker M, Brinkhoff T, Klenk HP. Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade. Stand Genomic Sci 2013; 9:128-41. [PMID: 24501651 PMCID: PMC3910543 DOI: 10.4056/sigs.4297965] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the type species of the genus Leisingera. The genus belongs to the Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed lineage in marine environments. Leisingera and particularly L. methylohalidivorans strain MB2(T) is of special interest due to its methylotrophy. Here we describe the complete genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. The 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists of three replicons, a single chromosome and two extrachromosomal elements with sizes of 221 kb and 285 kb.
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Affiliation(s)
- Nora Buddruhs
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St.Petersburg, Russia
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sabine Gronow
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Markus Göker
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
| | - Hans-Peter Klenk
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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15
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Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 2013; 9:142-59. [PMID: 24501652 PMCID: PMC3910554 DOI: 10.4056/sigs.4287962] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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16
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Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 2013. [DOI: 10.4056/sigs.3927626] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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17
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Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 2013; 8:403-19. [PMID: 24501626 PMCID: PMC3910702 DOI: 10.4056/sigs.3927623] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564T was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.
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Affiliation(s)
- Paul G Beyersmann
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
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18
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Freese HM, Dalingault H, Petersen J, Pradella S, Davenport K, Teshima H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Brinkhoff T, Göker M, Overmann J, Klenk HP. Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.). Stand Genomic Sci 2013; 8:450-64. [PMID: 24501630 PMCID: PMC3910698 DOI: 10.4056/sigs.383362] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members are phylogenetically and physiologically diverse. In contrast to the type species of this genus, Phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of P. arcticus. Here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. The 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists of one chromosome and five extrachromosomal elements. Prophage sequences identified via PHAST constitute nearly 5% of the bacterial chromosome and included a potential Mu-like phage as well as a gene-transfer agent (GTA). In addition, the genome of strain DSM 23566(T) encodes all of the genes necessary for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic distances indicate that the classification of the species might need to be reconsidered.
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Affiliation(s)
- Heike M. Freese
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Pradella
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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19
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Riedel T, Teshima H, Petersen J, Fiebig A, Davenport K, Daligault H, Erkkila T, Gu W, Munk C, Xu Y, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Göker M, Brinkhoff T, Klenk HP. Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci 2013; 8:389-402. [PMID: 24501625 PMCID: PMC3910692 DOI: 10.4056/sigs.3858183] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565(T) together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).
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Affiliation(s)
- Thomas Riedel
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Daligault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tracy Erkkila
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Wei Gu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Christine Munk
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Yan Xu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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20
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Neupane S, Goodwin LA, Högberg N, Kyrpides NC, Alström S, Bruce D, Quintana B, Munk C, Daligault H, Teshima H, Davenport K, Reitenga K, Green L, Chain P, Erkkila T, Gu W, Zhang X, Xu Y, Kunde Y, Chertkov O, Han J, Han C, Detter JC, Ivanova N, Pati A, Chen A, Szeto E, Mavromatis K, Huntemann M, Nolan M, Pitluck S, Deshpande S, Markowitz V, Pagani I, Klenk HP, Woyke T, Finlay RD. Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4. Stand Genomic Sci 2013; 8:441-9. [PMID: 24501629 PMCID: PMC3910699 DOI: 10.4056/sigs.4027757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project "Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI's Community Sequencing Program.
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Affiliation(s)
- Saraswoti Neupane
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Nils Högberg
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Sadhna Alström
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Beverly Quintana
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Christine Munk
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Daligault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Krista Reitenga
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lance Green
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tracy Erkkila
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Wei Gu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Xiaojing Zhang
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Yan Xu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Yulia Kunde
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Ernest Szeto
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roger D. Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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21
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Oosterkamp MJ, Veuskens T, Talarico Saia F, Weelink SAB, Goodwin LA, Daligault HE, Bruce DC, Detter JC, Tapia R, Han CS, Land ML, Hauser LJ, Langenhoff AAM, Gerritse J, van Berkel WJH, Pieper DH, Junca H, Smidt H, Schraa G, Davids M, Schaap PJ, Plugge CM, Stams AJM. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.). PLoS One 2013; 8:e66971. [PMID: 23825601 PMCID: PMC3692508 DOI: 10.1371/journal.pone.0066971] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/14/2013] [Indexed: 12/04/2022] Open
Abstract
The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.
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Affiliation(s)
| | - Teun Veuskens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Hajnalka E. Daligault
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - David C. Bruce
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - John C. Detter
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Roxanne Tapia
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Cliff S. Han
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Miriam L. Land
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Loren J. Hauser
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | | | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholz Centre for Infection Research, Braunschweig, Germany
| | - Howard Junca
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Bogotá, Colombia
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Gosse Schraa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- * E-mail:
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22
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Huntemann M, Stackebrandt E, Held B, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Woyke T, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Stand Genomic Sci 2013; 8:177-87. [PMID: 23991250 PMCID: PMC3746420 DOI: 10.4056/sigs.3637201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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23
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Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Pan C, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides NC, Klenk HP. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Stand Genomic Sci 2013; 8:228-38. [PMID: 23991255 PMCID: PMC3746428 DOI: 10.4056/sigs.3617113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was established as a result of the reclassification of Leptospira parva Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella constitutes the family Leptospiraceae, within the order Spirochaetales. Here we describe the features of this free-living aerobic spirochete together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Turneriella and the 13(th) member of the family Leptospiraceae for which a complete or draft genome sequence is now available. The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Erko Stackebrandt
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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24
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Liolos K, Abt B, Scheuner C, Teshima H, Held B, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Klenk HP, Kyrpides NC. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Stand Genomic Sci 2013; 8:165-76. [PMID: 23991249 PMCID: PMC3746417 DOI: 10.4056/sigs.3607108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817 protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.
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25
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Mavromatis K, Stackebrandt E, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Spring S, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Stand Genomic Sci 2013; 8:47-57. [PMID: 23961311 PMCID: PMC3739175 DOI: 10.4056/sigs.3547050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobaculum mobile Menes and Muxí 2002 is one of three described species of the genus Anaerobaculum, family Synergistaceae, phylum Synergistetes. This anaerobic and motile bacterium ferments a range of carbohydrates and mono- and dicarboxylic acids with acetate, hydrogen and CO2 as end products. A. mobile NGA(T) is the first member of the genus Anaerobaculum and the sixth member of the phylum Synergistetes with a completely sequenced genome. Here we describe the features of this bacterium, together with the complete genome sequence, and annotation. The 2,160,700 bp long single replicon genome with its 2,053 protein-coding and 56 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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26
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Stackebrandt E, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Chang YJ, Land M, Hauser L, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Stand Genomic Sci 2013; 8:15-25. [PMID: 23961308 PMCID: PMC3739169 DOI: 10.4056/sigs.3507020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Coriobacterium glomerans Haas and König 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2(T) is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for which complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Erko Stackebrandt
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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27
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Abt B, Göker M, Scheuner C, Han C, Lu M, Misra M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Rohde M, Spring S, Gronow S, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Woyke T, Klenk HP. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. Stand Genomic Sci 2013; 8:88-105. [PMID: 23961314 PMCID: PMC3739177 DOI: 10.4056/sigs.3096473] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain, H1(T), was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of interest because it enhances the degradation of cellulose when grown in co-culture with Clostridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassification of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional genomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1(T) with its 2,869 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Birte Abt
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Monica Misra
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nancy Hammon
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Cynthia D. Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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28
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Challacombe JF, Majid S, Deole R, Brettin TS, Bruce D, Delano SF, Detter JC, Gleasner CD, Han CS, Misra M, Reitenga KG, Mikhailova N, Woyke T, Pitluck S, Nolan M, Land ML, Saunders E, Tapia R, Lapidus A, Ivanova N, Hoff WD. Complete genome sequence of Halorhodospira halophila SL1. Stand Genomic Sci 2013; 8:206-14. [PMID: 23991253 PMCID: PMC3746430 DOI: 10.4056/sigs.3677284] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halorhodospira halophila is among the most halophilic organisms known. It is an obligately photosynthetic and anaerobic purple sulfur bacterium that exhibits autotrophic growth up to saturated NaCl concentrations. The type strain H. halophila SL1 was isolated from a hypersaline lake in Oregon. Here we report the determination of its entire genome in a single contig. This is the first genome of a phototrophic extreme halophile. The genome consists of 2,678,452 bp, encoding 2,493 predicted genes as determined by automated genome annotation. Of the 2,407 predicted proteins, 1,905 were assigned to a putative function. Future detailed analysis of this genome promises to yield insights into the halophilic adaptations of this organism, its ability for photoautotrophic growth under extreme conditions, and its characteristic sulfur metabolism.
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Affiliation(s)
- Jean F Challacombe
- Los Alamos National Laboratory and DOE Joint Genome Institute, Bioscience Division, Los Alamos, New Mexico, USA
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29
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Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Han C, Cheng JF, Tapia R, Goodwin LA, Bruce D, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Stand Genomic Sci 2013; 8:37-46. [PMID: 23961310 PMCID: PMC3739173 DOI: 10.4056/sigs.3537045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
At present, Joostella marina Quan et al. 2008 is the sole species with a validly published name in the genus Joostella, family Flavobacteriacae, phylum Bacteriodetes. It is a yellow-pigmented, aerobic, marine organism about which little has been reported other than the chemotaxonomic features required for initial taxonomic description. The genome of J. marina strain En5(T) complements a list of 16 Flavobacteriaceae strains for which complete genomes and draft genomes are currently available. Here we describe the features of this bacterium, together with the complete genome sequence, and annotation. This is the first member of the genus Joostella for which a complete genome sequence becomes available. The 4,508,243 bp long single replicon genome with its 3,944 protein-coding and 60 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Erko Stackebrandt
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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30
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Mavromatis K, Stackebrandt E, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Stand Genomic Sci 2013; 8:26-36. [PMID: 23961309 PMCID: PMC3739176 DOI: 10.4056/sigs.3527032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with a validly published name: family Rikenellaceae, order Bacteroidetes, class Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic organism has been isolated mostly from human tissues. Here we describe the features of the type strain of this species, together with the complete genome sequence, and annotation. A. finegoldii is the first member of the genus Alistipes for which the complete genome sequence of its type strain is now available. The 3,734,239 bp long single replicon genome with its 3,302 protein-coding and 68 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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31
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Fitzsimons MS, Novotny M, Lo CC, Dichosa AEK, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res 2013; 23:878-88. [PMID: 23493677 PMCID: PMC3638143 DOI: 10.1101/gr.142208.112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
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Affiliation(s)
- Michael S Fitzsimons
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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32
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Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han C, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Peters L, Pitluck S, Lam J, McDonald AI, Dodsworth JA, Woyke T, Hedlund BP. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Stand Genomic Sci 2013; 7:449-68. [PMID: 24019992 PMCID: PMC3764938 DOI: 10.4056/sigs.3667269] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18 chromosome with those from other strains of T. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no synteny with other sequenced Thermus strains. Phylogenomic analyses using a concatenated set of conserved proteins confirmed the phylogenetic and taxonomic assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus glucosidases, glycosidases, proteases, and peptidases, highlighting highly versatile heterotrophic capabilities. Megaplasmids of both strains contained a gene cluster encoding enzymes predicted to catalyze the sequential reduction of nitrate to nitrous oxide; however, the nitrous oxide reductase required for the terminal step in denitrification was absent, consistent with their incomplete denitrification phenotypes. A sox gene cluster was identified in both chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and polysulfide reduction as possible modes of anaerobic respiration.
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33
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Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Stand Genomic Sci 2012; 7:210-20. [PMID: 23408178 PMCID: PMC3569382 DOI: 10.4056/sigs.3117229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8(T) is of interest for its ability to produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T) is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
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34
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Spring S, Visser M, Lu M, Copeland A, Lapidus A, Lucas S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Ivanova N, Land M, Hauser L, Larimer F, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T, Schaap PJ, Plugge CM, Muyzer G, Kuever J, Pereira IAC, Parshina SN, Bernier-Latmani R, Stams AJM, Klenk HP. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)). Stand Genomic Sci 2012; 7:304-19. [PMID: 23408247 PMCID: PMC3569383 DOI: 10.4056/sigs.3226659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.
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Affiliation(s)
- Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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35
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Neupane S, Finlay RD, Kyrpides NC, Goodwin L, Alström S, Lucas S, Land M, Han J, Lapidus A, Cheng JF, Bruce D, Pitluck S, Peters L, Ovchinnikova G, Held B, Han C, Detter JC, Tapia R, Hauser L, Ivanova N, Pagani I, Woyke T, Klenk HP, Högberg N. Complete genome sequence of the plant-associated Serratia plymuthica strain AS13. Stand Genomic Sci 2012; 7:22-30. [PMID: 23450001 PMCID: PMC3570797 DOI: 10.4056/sigs.2966299] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens" within the 2010 DOE-JGI Community Sequencing Program (CSP2010).
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Affiliation(s)
- Saraswoti Neupane
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger D. Finlay
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sadhna Alström
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lin Peters
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Brittany Held
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nils Högberg
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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36
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Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Detter JC, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Stand Genomic Sci 2012; 7:120-30. [PMID: 23450211 PMCID: PMC3570807 DOI: 10.4056/sigs.3296896] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Owenweeksia hongkongensis Lau et al. 2005 is the sole member of the monospecific genus Owenweeksia in the family Cryomorphaceae, a poorly characterized family at the genome level thus far. This family comprises seven genera within the class Flavobacteria. Family members are known to be psychrotolerant, rod-shaped and orange pigmented (β-carotene), typical for Flavobacteria. For growth, seawater and complex organic nutrients are necessary. The genome of O. hongkongensis UST20020801(T) is only the second genome of a member of the family Cryomorphaceae whose sequence has been deciphered. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,000,057 bp long chromosome with its 3,518 protein-coding and 45 RNA genes is a part of the GenomicEncyclopedia ofBacteriaandArchaea project.
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Affiliation(s)
- Thomas Riedel
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Brittany Held
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Brian J. Tindall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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37
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Kappler U, Davenport K, Beatson S, Lucas S, Lapidus A, Copeland A, Berry KW, Glavina Del Rio T, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin LA, Han C, Tapia R, Detter JC, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Göker M, Ivanova N, Klenk HP, Woyke T. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)). Stand Genomic Sci 2012; 7:44-58. [PMID: 23450099 PMCID: PMC3570799 DOI: 10.4056/sigs.3006378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order 'Rhizobiales', which is thus far poorly characterized at the genome level. Cultures from this species are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. This feature makes S. novella an interesting model organism for studying the genomic basis of regulatory networks required for the switch between consumption and production of carbon dioxide, a key component of the global carbon cycle. In addition, S. novella is of interest for its ability to grow on various inorganic sulfur compounds and several C1-compounds such as methanol. Besides Azorhizobium caulinodans, S. novella is only the second species in the family Xanthobacteraceae with a completely sequenced genome of a type strain. The current taxonomic classification of this group is in significant conflict with the 16S rRNA data. The genomic data indicate that the physiological capabilities of the organism might have been underestimated. The 4,765,023 bp long chromosome with its 4,511 protein-coding and 52 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
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Affiliation(s)
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Nancy Hammon
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yun-juan Chang
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Cynthia D. Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
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38
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Riedel T, Held B, Nolan M, Lucas S, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Stand Genomic Sci 2012; 7:107-19. [PMID: 23450183 PMCID: PMC3570806 DOI: 10.4056/sigs.3216895] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G. limnea R-8282(T) is the first sequenced genome (permanent draft) from a type strain of the genus Gillisia. Here we describe the features of this organism, together with the permanent-draft genome sequence and annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569 protein-coding and 51 RNA genes is a part of the GenomicEncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Thomas Riedel
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
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39
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Kappler U, Davenport K, Beatson S, Lucas S, Lapidus A, Copeland A, Berry KW, Glavina Del Rio T, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin LA, Han C, Tapia R, Detter JC, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Göker M, Ivanova N, Klenk HP, Woyke T. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T). Stand Genomic Sci 2012. [DOI: 10.4056/sogs.3006378] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Karen Davenport
- 2Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Susan Lucas
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Nancy Hammon
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Eileen Dalin
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Bruce
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Cliff Han
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C. Detter
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yun-juan Chang
- 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Miriam Land
- 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Markus Göker
- 5Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Hans-Peter Klenk
- 5Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
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40
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Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Stand Genomic Sci 2012; 6:381-400. [PMID: 23408395 PMCID: PMC3558958 DOI: 10.4056/sigs.2605792] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.
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Affiliation(s)
- David A. Mead
- Lucigen Corporation, Middleton, Wisconsin
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - David C. Bruce
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Sam Pitluck
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Olga Chertkov
- DOE Joint Genome Institute, Walnut Creek, California
| | - Xiaojing Zhang
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Cliff S. Han
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Loren J. Hauser
- DOE Joint Genome Institute, Walnut Creek, California
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California
| | | | | | | | - Phillip Brumm
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
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41
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Jiang K, Sanseverino J, Chauhan A, Lucas S, Copeland A, Lapidus A, Del Rio TG, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Sims D, Brettin T, Detter JC, Han C, Chang YJ, Larimer F, Land M, Hauser L, Kyrpides NC, Mikhailova N, Moser S, Jegier P, Close D, Debruyn JM, Wang Y, Layton AC, Allen MS, Sayler GS. Complete genome sequence of Thauera aminoaromatica strain MZ1T. Stand Genomic Sci 2012; 6:325-35. [PMID: 23407619 PMCID: PMC3558969 DOI: 10.4056/sigs.2696029] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Sequencing Program CSP_776774.
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Affiliation(s)
- Ke Jiang
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Tennessee, USA
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42
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Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci 2012; 6:1-13. [PMID: 23407703 PMCID: PMC3558970 DOI: 10.4056/sigs.2736042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the GenomicEncyclopedia ofBacteria andArchaea project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
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43
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Mavromatis K, Chertkov O, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Bruce D, Goodwin LA, Pitluck S, Huntemann M, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Stand Genomic Sci 2012; 6:210-9. [PMID: 22768364 PMCID: PMC3387799 DOI: 10.4056/sigs.2816096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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44
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Neupane S, Finlay RD, Alström S, Goodwin L, Kyrpides NC, Lucas S, Lapidus A, Bruce D, Pitluck S, Peters L, Ovchinnikova G, Chertkov O, Han J, Han C, Tapia R, Detter JC, Land M, Hauser L, Cheng JF, Ivanova N, Pagani I, Klenk HP, Woyke T, Högberg N. Complete genome sequence of Serratia plymuthica strain AS12. Stand Genomic Sci 2012; 6:165-73. [PMID: 22768360 PMCID: PMC3387793 DOI: 10.4056/sigs.2705996] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens".
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45
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Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao ODN, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci 2012; 6:145-54. [PMID: 22768358 PMCID: PMC3387789 DOI: 10.4056/sigs.2475579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the Cytophagaceae, a family that was only recently classified to the order Cytophagales in the class Cytophagia. The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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46
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Klenk HP, Held B, Lucas S, Lapidus A, Copeland A, Hammon N, Pitluck S, Goodwin LA, Han C, Tapia R, Brambilla EM, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)). Stand Genomic Sci 2012; 6:220-9. [PMID: 22768365 PMCID: PMC3387790 DOI: 10.4056/sigs.2635833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Saccharomonospora azurea Runmao et al. 1987 is a member of the genus Saccharomonospora, which is in the family Pseudonocardiaceae and thus far poorly characterized genomically. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, the surface of peat, and moist and over-heated grain, and may play a role in the primary degradation of plant material by attacking hemicellulose. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for which a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'Improved high quality draft', and the annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
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47
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Anderson I, Saunders E, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Chang YJ, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Stand Genomic Sci 2012; 6:155-64. [PMID: 22768359 PMCID: PMC3387792 DOI: 10.4056/sigs.2665915] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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48
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Klenk HP, Lu M, Lucas S, Lapidus A, Copeland A, Pitluck S, Goodwin LA, Han C, Tapia R, Brambilla EM, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Li WJ, Kyrpides NC, Woyke T. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)). Stand Genomic Sci 2012; 6:265-75. [PMID: 22768369 PMCID: PMC3387791 DOI: 10.4056/sigs.2655905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Saccharomonospora marina Liu et al. 2010 is a member of the genus Saccharomonospora, in the family Pseudonocardiaceae that is poorly characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Here we describe the features of this organism, together with the complete genome sequence (permanent draft status), and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
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49
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Göker M, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Spring S, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Stand Genomic Sci 2012; 6:230-9. [PMID: 22768366 PMCID: PMC3387794 DOI: 10.4056/sigs.2726028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thermovirga lienii Dahle and Birkeland 2006 is a member of the genus Thermovirga in the genomically moderately well characterized phylum 'Synergistetes'. Members of this relatively recently proposed phylum 'Synergistetes' are of interest because of their isolated phylogenetic position and their diverse habitats, e.g. from humans to oil wells. The genome of T. lienii Cas60314(T) is the fifth genome sequence (third completed) from this phylum to be published. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,999,646 bp long genome (including one plasmid) with its 1,914 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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50
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Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Rohde M, Spring S, Gronow S, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci 2012; 6:194-209. [PMID: 22768363 PMCID: PMC3388779 DOI: 10.4056/sigs.2796069] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Spirochaeta coccoides Dröge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1(T), and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1(T) with its 1,866 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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