Microbial Diversity of Soda Lake Habitats

Total Page:16

File Type:pdf, Size:1020Kb

Microbial Diversity of Soda Lake Habitats Microbial Diversity of Soda Lake Habitats Von der Gemeinsamen Naturwissenschaftlichen Fakultät der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Susanne Baumgarte aus Fritzlar 1. Referent: Prof. Dr. K. N. Timmis 2. Referent: Prof. Dr. E. Stackebrandt eingereicht am: 26.08.2002 mündliche Prüfung (Disputation) am: 10.01.2003 2003 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Gemeinsamen Naturwissenschaftlichen Fakultät, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Baumgarte, S., Moore, E. R. & Tindall, B. J. (2001). Re-examining the 16S rDNA sequence of Halomonas salina. International Journal of Systematic and Evolutionary Microbiology 51: 51-53. Tagungsbeiträge Baumgarte, S., Mau, M., Bennasar, A., Moore, E. R., Tindall, B. J. & Timmis, K. N. (1999). Archaeal diversity in soda lake habitats. (Vortrag). Jahrestagung der VAAM, Göttingen. Baumgarte, S., Tindall, B. J., Mau, M., Bennasar, A., Timmis, K. N. & Moore, E. R. (1998). Bacterial and archaeal diversity in an African soda lake. (Poster). Körber Symposium on Molecular and Microsensor Studies of Microbial Communities, Bremen. II Contents 1. Introduction............................................................................................................... 1 1.1. The soda lake environment .................................................................................. 1 1.2. Microbial diversity of soda lakes ......................................................................... 8 1.3. Ribosomal RNA(-genes) and molecular microbial ecology.................................16 1.4. Aim of the project...............................................................................................23 2. Materials and methods.............................................................................................24 2.1. Samples........ ......................................................................................................24 2.2. Extraction of DNA..............................................................................................25 2.2.1. Preparation of genomic DNA from pure cultures of bacteria .......................25 2.2.2. Rapid preparation of genomic DNA from bacterial colonies........................25 2.2.3. Extraction of DNA from sediment samples..................................................26 2.2.4. Determination of DNA concentration ..........................................................27 2.3. Polymerase chain reaction (PCR)........................................................................27 2.3.1. Purification of PCR products.......................................................................28 2.3.2. Oligonucleotide primers for PCR ................................................................29 2.4. Cloning of amplified 16S rDNA .........................................................................30 2.4.1. Blue/white screening for recombinant plasmids...........................................30 2.4.2. Size screening for recombinant plasmids.....................................................30 2.4.3. Storage of clones .........................................................................................31 2.4.4. Preparation of plasmid DNA .......................................................................31 2.5. 16S rDNA sequencing ........................................................................................31 2.5.1. Thermocycler protocol ................................................................................32 2.5.2. Purification of extension products ...............................................................32 III 2.5.3. Analysis of sequence data............................................................................32 2.6. DNA hybridisation..............................................................................................32 2.6.1. Dot blotting of DNA....................................................................................32 2.6.2. Dot blot pre-hybridisation and hybridisation ...............................................33 2.6.3. Stringency washing .....................................................................................33 2.6.4. Chemiluminescense detection......................................................................34 2.6.5. Rehybridisation ...........................................................................................34 2.6.6. Oligonucleotide probes................................................................................34 2.7. Amplified ribosomal DNA restriction analysis (ARDRA) ..................................34 3. Results and discussion..............................................................................................36 3.1. Screening of 16S rDNA molecules .....................................................................36 3.1.1. DNA sequencing .........................................................................................36 3.1.2. Fingerprinting analysis ................................................................................36 3.1.3. Non-radioactive colony hybridisation..........................................................38 3.2. Cultivation-independent analysis of microbial diversity .....................................42 3.2.1. Extraction of DNA ......................................................................................42 3.2.2. PCR amplification .......................................................................................44 3.2.3. Cloning .......................................................................................................45 3.2.3.1. Generation of 16S rDNA clone libraries from serial-diluted DNA ....................................................................................................45 3.2.3.2. Regeneration of a ligation-independent cloning (LIC) vector...............46 3.2.4. Analysis of the predominant bacterial 16S rDNA sequence types................55 3.2.4.1. Predominance of sequence types of the Cyanobacteria ........................57 3.2.4.2. Sequence types related to the Firmicutes..............................................65 3.2.4.2.1. Sequence types related to the Bacilli .............................................. 65 3.2.4.2.2. Sequence types related to the Clostridia......................................... 70 3.2.4.3. Sequence types related to the Proteobacteria.......................................78 IV 3.2.4.3.1. Sequence types related to the Alpha-Proteobacteria....................... 78 3.2.4.3.2. Sequence types related to the Gamma-Proteobacteria.................... 79 3.2.4.3.3. Sequence types related to the Delta-Proteobacteria ....................... 85 3.2.4.4. Sequence types related to the Bacteroidetes.........................................85 3.2.5. Analysis of the “overall” diversity of bacterial 16S rDNA sequences..........87 3.2.5.1. Non-radioactive colony and dot-blot hybridisations .............................87 3.2.5.2. ARDRA fingerprinting.........................................................................88 3.2.5.3. 16S rDNA sequence determination.......................................................89 3.2.5.3.1. Sequence types related to the Bacilli .............................................. 92 3.2.5.3.2. Sequence types related to the Clostridia......................................... 93 3.2.5.3.3. Sequence types related to the Alpha-Proteobacteria....................... 98 3.2.5.3.4. Sequence types related to the Gamma-Proteobacteria.................... 99 3.2.5.3.5. Sequence types related to the Delta-Proteobacteria ..................... 101 3.2.5.3.6. Sequence types related to the Bacteroidetes ................................. 102 3.2.5.3.7. Chimeric sequences ...................................................................... 102 3.2.6. Analysis of the archaeal 16S rDNA clone library ......................................106 3.2.6.1. ARDRA fingerprinting.......................................................................106 3.2.6.2. 16S rDNA sequence determination.....................................................107 3.2.7. Statistical approaches to estimating 16S rDNA sequence diversity............116 3.3. Cultivation-dependent analysis of microbial diversity ......................................122 3.3.1. Analysis of Archaea isolates derived from other haloalkaline environments .............................................................................................122 3.3.1.1. Halobacteria.......................................................................................122 3.3.1.2. ARDRA fingerprinting.......................................................................125 3.3.1.3. 16S rDNA sequence determination.....................................................129 3.3.2. Analysis of aerobic sporeformers isolated from soda lake samples............136 3.3.2.1. ARDRA fingerprinting.......................................................................136 3.3.2.2. 16S rDNA sequence determination.....................................................137 3.3.3. Analysis of a unicellular cyanobacterium isolated from Lake Magadi .......141 3.3.3.1. Generation of a 16S rDNA clone library ............................................142 V 3.3.3.2. Screening of transformants by using colony hybridisation
Recommended publications
  • Actinobacterial Diversity of the Ethiopian Rift Valley Lakes
    ACTINOBACTERIAL DIVERSITY OF THE ETHIOPIAN RIFT VALLEY LAKES By Gerda Du Plessis Submitted in partial fulfillment of the requirements for the degree of Magister Scientiae (M.Sc.) in the Department of Biotechnology, University of the Western Cape Supervisor: Prof. D.A. Cowan Co-Supervisor: Dr. I.M. Tuffin November 2011 DECLARATION I declare that „The Actinobacterial diversity of the Ethiopian Rift Valley Lakes is my own work, that it has not been submitted for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged by complete references. ------------------------------------------------- Gerda Du Plessis ii ABSTRACT The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomic studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites.
    [Show full text]
  • History of the Chlor-Alkali Industry
    2 History of the Chlor-Alkali Industry During the last half of the 19th century, chlorine, used almost exclusively in the textile and paper industry, was made [1] by reacting manganese dioxide with hydrochloric acid 100–110◦C MnO2 + 4HCl −−−−−−→ MnCl2 + Cl2 + 2H2O (1) Recycling of manganese improved the overall process economics, and the process became known as the Weldon process [2]. In the 1860s, the Deacon process, which generated chlorine by direct catalytic oxidation of hydrochloric acid with air according to Eq. (2) was developed [3]. ◦ 450–460 C;CuCl2 cat. 4HCl + O2(air) −−−−−−−−−−−−−−→ 2Cl2 + 2H2O(2) The HCl required for reactions (1) and (2) was available from the manufacture of soda ash by the LeBlanc process [4,5]. H2SO4 + 2NaCl → Na2SO4 + 2HCl (3) Na2SO4 + CaCO3 + 2C → Na2CO3 + CaS + 2CO2 (4) Utilization of HCl from reaction (3) eliminated the major water and air pollution problems of the LeBlanc process and allowed the generation of chlorine. By 1900, the Weldon and Deacon processes generated enough chlorine for the production of about 150,000 tons per year of bleaching powder in England alone [6]. An important discovery during this period was the fact that steel is immune to attack by dry chlorine [7]. This permitted the first commercial production and distribu- tion of dry liquid chlorine by Badische Anilin-und-Soda Fabrik (BASF) of Germany in 1888 [8,9]. This technology, using H2SO4 for drying followed by compression of the gas and condensation by cooling, is much the same as is currently practiced. 17 “chap02” — 2005/5/2 — 09Brie:49 — page 17 — #1 18 CHAPTER 2 In the latter part of the 19th century, the Solvay process for caustic soda began to replace the LeBlanc process.
    [Show full text]
  • Correction: Genomic Comparison of 93 Bacillus Phages Reveals 12 Clusters
    Grose et al. BMC Genomics 2014, 15:1184 http://www.biomedcentral.com/1471-2164/15/1184 CORRECTION Open Access Correction: genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity Julianne H Grose*, Garrett L Jensen, Sandra H Burnett and Donald P Breakwell Abstract Background: The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. Results: Whole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function.
    [Show full text]
  • Isolation and Characterization of Achromobacter Sp. CX2 From
    Ann Microbiol (2015) 65:1699–1707 DOI 10.1007/s13213-014-1009-6 ORIGINAL ARTICLE Isolation and characterization of Achromobacter sp. CX2 from symbiotic Cytophagales, a non-cellulolytic bacterium showing synergism with cellulolytic microbes by producing β-glucosidase Xiaoyi Chen & Ying Wang & Fan Yang & Yinbo Qu & Xianzhen Li Received: 27 August 2014 /Accepted: 24 November 2014 /Published online: 10 December 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract A Gram-negative, obligately aerobic, non- degradation by cellulase (Carpita and Gibeaut 1993). There- cellulolytic bacterium was isolated from the cellulolytic asso- fore, efficient degradation is the result of multiple activities ciation of Cytophagales. It exhibits biochemical properties working synergistically to efficiently solubilize crystalline cel- that are consistent with its classification in the genus lulose (Sánchez et al. 2004;Lietal.2009). Most known Achromobacter. Phylogenetic analysis together with the phe- cellulolytic organisms produce multiple cellulases that act syn- notypic characteristics suggest that the isolate could be a novel ergistically on native cellulose (Wilson 2008)aswellaspro- species of the genus Achromobacter and designated as CX2 (= duce some other proteins that enhance cellulose hydrolysis CGMCC 1.12675=CICC 23807). The strain CX2 is the sym- (Wang et al. 2011a, b). Synergistic cooperation of different biotic microbe of Cytophagales and produces β-glucosidase. enzymes is a prerequisite for the efficient degradation of cellu- The results showed that the non-cellulolytic Achromobacter lose (Jalak et al. 2012). Both Trichoderma reesi and Aspergillus sp. CX2 has synergistic activity with cellulolytic microbes by niger were co-cultured to increase the levels of different enzy- producing β-glucosidase.
    [Show full text]
  • Suppression Mechanisms of Alkali Metal Compounds
    SUPPRESSION MECHANISMS OF ALKALI METAL COMPOUNDS Bradley A. Williams and James W. Fleming Chemistry Division, Code 61x5 US Naval Research Lnhoratory Washington, DC 20375-5342, USA INTRODUCTION Alkali metal compounds, particularly those of sodium and potassium, are widely used as fire suppressants. Of particular note is that small NuHCOi particles have been found to be 2-4 times more effective by mass than Halon 1301 in extinguishing both eountertlow flames [ I] and cup- burner flames [?]. Furthermore, studies in our laboratory have found that potassium bicarbonate is some 2.5 times more efficient by weight at suppression than sodium bicarhonatc. The primary limitation associated with the use of alkali metal compounds is dispersal. since all known compounds have very low volatility and must he delivered to the fire either as powders or in (usually aqueous) solution. Although powders based on alkali metals have been used for many years, their mode of effective- ness has not generally been agreed upon. Thermal effects [3],namely, the vaporization of the particles as well as radiative energy transfer out of the flame. and both homogeneous (gas phase) and heterogeneous (surface) chemistry have been postulated as mechanisms by which alkali metals suppress fires [4]. Complicating these issues is the fact that for powders, particle size and morphology have been found to affect the suppression properties significantly [I]. In addition to sodium and potassium, other alkali metals have been studied, albeit to a consider- ably lesser extent. The general finding is that the suppression effectiveness increases with atomic weight: potassium is more effective than sodium, which is in turn more effective than lithium [4].
    [Show full text]
  • Bacillus Crassostreae Sp. Nov., Isolated from an Oyster (Crassostrea Hongkongensis)
    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1561–1566 DOI 10.1099/ijs.0.000139 Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis) Jin-Hua Chen,1,2 Xiang-Rong Tian,2 Ying Ruan,1 Ling-Ling Yang,3 Ze-Qiang He,2 Shu-Kun Tang,3 Wen-Jun Li,3 Huazhong Shi4 and Yi-Guang Chen2 Correspondence 1Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Yi-Guang Chen Hunan Agricultural University, 410128 Changsha, PR China mchenjsu@aliyun.com 2College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China 3The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China 4Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 6C (optimum 30–35 6C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0,C16 : 0 and C16 : 1v11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%.
    [Show full text]
  • Identification of Salt Accumulating Organisms from Winery Wastewater
    Identification of salt accumulating organisms from winery wastewater FINAL REPORT to GRAPE AND WINE RESEARCH & DEVELOPMENT CORPORATION Project Number: UA08/01 Principal Investigator: Paul Grbin Research Organisation: University of Adelaide Date: 22/09/10 1 Identification of salt accumulating organisms from winery wastewater Dr Paul R Grbin Dr Kathryn L Eales Dr Frank Schmid Assoc. Prof. Vladimir Jiranek The University of Adelaide School of Agriculture, Food and Wine PMB 1, Glen Osmond, SA 5064 AUSTRALIA Date: 15 January 2010 Publisher: University of Adelaide Disclaimer: The advice presented in this document is intended as a source of information only. The University of Adelaide (UA) accept no responsibility for the results of any actions taken on the basis of the information contained within this publication, nor for the accuracy, currency or completeness of any material reported and therefore disclaim all liability for any error, loss or other consequence which may arise from relying on information in this publication. 2 Table of contents Abstract 3 Executive Summary 4 Background 5 Project Aims and Performance Targets 6 Methods 7 Results and Discussion 11 Outcomes and Conclusions 23 Recommendations 24 Appendix 1: Communication Appendix 2: Intellectual Property Appendix 3: References Appendix 4: Staff Appendix 5: Acknowledgements Appendix 6: Budget Reconciliation 3 Abbreviations: COD: Chemical oxygen demand Ec: Electrical conductivity FACS: Fluorescence activated cell sorting HEPES: 4‐(2‐hydroxyethyl)‐1‐piperazineethanesulfonic acid OD: Optical density PBFI: Potassium benzofuran isophthalate PI: Propidium iodide SAR: Sodium adsorption ratio WWW: Winery wastewater Abstract: In an attempt to find microorganisms that would remove salts from biological winery wastewater (WWW) treatment plants, 8 halophiles were purchased from culture collections, with a further 40 isolated from WWW plants located in the Barossa Valley and McLaren Vale regions.
    [Show full text]
  • Identification of Active Methylotroph Populations in an Acidic Forest Soil
    Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria.
    [Show full text]
  • Alkali-Silica Reactivity: an Overview of Research
    SHRP-C-342 Alkali-Silica Reactivity: An Overview of Research Richard Helmuth Construction Technology Laboratories, Inc. With contributions by: David Stark Construction Technology Laboratories, Inc. Sidney Diamond Purdue University Micheline Moranville-Regourd Ecole Normale Superieure de Cachan Strategic Highway Research Program National Research Council Washington, DC 1993 Publication No. SHRP-C-342 ISBN 0-30cL05602-0 Contract C-202 Product No. 2010 Program Manager: Don M. Harriott Project Maxtager: Inam Jawed Program AIea Secretary: Carina Hreib Copyeditor: Katharyn L. Bine Brosseau May 1993 key words: additives aggregate alkali-silica reaction cracking expansion portland cement concrete standards Strategic Highway Research Program 2101 Consti!ution Avenue N.W. Washington, DC 20418 (202) 334-3774 The publicat:Lon of this report does not necessarily indicate approval or endorsement by the National Academy of Sciences, the United States Government, or the American Association of State Highway and Transportation Officials or its member states of the findings, opinions, conclusions, or recommendations either inferred or specifically expressed herein. ©1993 National Academy of Sciences 1.5M/NAP/593 Acknowledgments The research described herein was supported by the Strategic Highway Research Program (SHRP). SHRP is a unit of the National Research Council that was authorized by section 128 of the Surface Transportation and Uniform Relocation Assistance Act of 1987. This document has been written as a product of Strategic Highway Research Program (SHRP) Contract SHRP-87-C-202, "Eliminating or Minimizing Alkali-Silica Reactivity." The prime contractor for this project is Construction Technology Laboratories, with Purdue University, and Ecole Normale Superieure de Cachan, as subcontractors. Fundamental studies were initiated in Task A.
    [Show full text]
  • Exploring Bacteria Diatom Associations Using Single-Cell
    Vol. 72: 73–88, 2014 AQUATIC MICROBIAL ECOLOGY Published online April 4 doi: 10.3354/ame01686 Aquat Microb Ecol FREEREE ACCESSCCESS Exploring bacteria–diatom associations using single-cell whole genome amplification Lydia J. Baker*, Paul F. Kemp Department of Oceanography, University of Hawai’i at Manoa, 1950 East West Road, Center for Microbial Oceanography: Research and Education (C-MORE), Honolulu, Hawai’i 96822, USA ABSTRACT: Diatoms are responsible for a large fraction of oceanic and freshwater biomass pro- duction and are critically important for sequestration of carbon to the deep ocean. As with most surfaces present in aquatic systems, bacteria colonize the exterior of diatom cells, and they inter- act with the diatom and each other. The ecology of diatoms may be better explained by conceptu- alizing them as composite organisms consisting of the host cell and its bacterial associates. Such associations could have collective properties that are not predictable from the properties of the host cell alone. Past studies of these associations have employed culture-based, whole-population methods. In contrast, we examined the composition and variability of bacterial assemblages attached to individual diatoms. Samples were collected in an oligotrophic system (Station ALOHA, 22° 45’ N, 158° 00’ W) at the deep chlorophyll maximum. Forty eukaryotic host cells were isolated by flow cytometry followed by multiple displacement amplification, including 26 Thalassiosira spp., other diatoms, dinoflagellates, coccolithophorids, and flagellates. Bacteria were identified by amplifying, cloning, and sequencing 16S rDNA using primers that select against chloroplast 16S rDNA. Bacterial sequences were recovered from 32 of 40 host cells, and from parallel samples of the free-living and particle-associated bacteria.
    [Show full text]
  • Granulicella Tundricola Type Strain MP5ACTX9T, an Acidobacteria from Tundra Soil
    Standards in Genomic Sciences (2014) 9:449-461 DOI:10.4056/sig s.4648353 Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil Suman R. Rawat1, Minna K. Männistö 2, Valentin Starovoytov3, Lynne Goodwin4, Matt Nolan5 Loren Hauser6, Miriam Land 6, Karen Walston Davenport4, Tanja Woyke5 and Max M. Häggblom1* 1 Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey USA 2 Finnish Forest Research Institute, Rovaniemi, Finland 3 Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA. 4 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 5 DOE Joint Genome Institute, Walnut Creek, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA *Correspondence: Max M Häggblom (haggblom@sebs.rutgers.edu) Keywords: cold adapted, acidophile, tundra soil, Acidobacteria Granulicella tundricola strain MP5ACTX9T is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism is a cold-adapted acidophile and a versatile heterotroph that hydro- lyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including g ene modules encoding for the carbohydrate-active enzyme (CAZy) families for the break- down, utilization and biosy nthesis of diverse structural and storag e polysaccharides suc h as plant based carbon polymers. The g enome of G. tundricola strain MP5ACTX9T consists of 4,309,151 bp of a circular chromosome and five meg a plasmids with a total genome con- tent of 5,503,984 bp.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]