DOCSLIB.ORG

Download the File

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Download the File CALIFORNIA STATE UNIVERSITY SAN MARCOS THESIS SIGNATURE PAGE THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE MASTER OF SCIENCE IN BIOLOGICAL SCIENCES THESIS TITLE: The Isolation and Characterization ofa Novel Haloalkaliphilic Purple Sulfur Bacterium, Ectothiorhodospira monomense, sp. nov., from Mono Lake AUTHOR: Crista DiBernardo DATE OF SUCCESSFUL DEFENSE: May 25, 2001 THE THESIS HAS BEEN ACCEPTED BY THE THESIS COMMITTEE IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN BIOLOGICAL SCIENCES. Thomas Wahlund, Ph.D. ~idJ-fJ{.Wt<-~aY25'OI THESIS COMMITTEE CHAIR (TYPED) SIGNATURE DATE Betsy Read, Ed.D. ~a R~c~ May25,01 THESIS COMMITTEE MEMBER (TYPED) SI URE DATE Victoria Fabry, Ph.D. THESIS COMMITTEE MEMBER (TYPED) ii The Isolation and Characterization of a Novel Haloalkaliphilic Purple Sulfur Bacterium, Ectothiorhodospira monomense, sp. nov., from Mono Lake by Crista Danielle DiBernardo Bachelor of Science, Biological Sciences A thesis written in partial fulfillment of the requirements for Master of Science in Biological Sciences Department of Graduate Studies California State University San Marcos June 2001 iii ACKNOWLEDGMENTS Getting a Master's Degree has been an experience that I never would have made it through without the support and encouragement of family and friends. It is because of you that this thesis is finally published. Thank you, from the bottom of my heart! Dr. Tom Wahlund, thanks for taking on a graduate student, wholly uneducated in microbiology, and teaching me to love germs! Your support, feedback and high expectations have helped me to look back on the past few years with pride and accomplishment. Dr. Betsy Read, your encouragement and support from the moment I stepped foot on CSU San Marcos soil have meant more than you will ever know. Thank you for always being there with advice, moral support and pom-poms when needed. Dr. Vicki Fabry, you've always made me feel accomplished and worthy of any challenge, both scholastic and personal. Thank you for always believing in me. To Shannon and Alicia, who have easily spent hours in complete silence listening to my complaints, and commiserating with me even when I was at my most irrational. To Jason and Dande, for making life in Science Hall fun. To Jose, Mike and Kevin whose friendships remind me that there's more to life than biology. Thanks! Huge thanks to Jenni & Mario, for believing in me and giving me a place to call home. To my little brother Mario, thank you for always thinking I'm the smartest person in the world, true or not. iv Above all, I thank my parents for their support, love and belief that I could do anything. To my Dad; whose childhood dreams of being a scientist inspired my reality. And to my Mom; whose hugs & encouragement still make everything all right, even when you're 27. v ABSTRACT Life exists in a wide range of environments with prokaryotic organisms inhabiting those considered most hostile, including extremes of temperature, salinity, water activity, and pH. The microorganisms that inhabit these extreme environments, and in particular anoxygenic phototrophs that inhabit salt and soda lakes, are the focus of this thesis. These environments are typified by (1) high salinity, and the associated problem of a hypoosmotic external environment, and (2) an alkaline environment, where the cell's membrane potential is disrupted. In the present study, a novel purple sulfur bacterium of the genus Ectothiorhodospira was isolated from the highly saline (8%) highly alkaline (pH 8-10) Mono Lake in Mono County, CA. This isolate exhibited optimal growth under photoheterotrophic conditions at 1.4 M NaCl and pH 9.4, and possessed many metabolic properties unique among related organisms. The classification of the organism isolated in this study, Ectothiorhodospira strain MLS1, as a novel species, Ectothiorhodospira monomense (N.L. adj. pertaining to Mono Lake), is thus proposed. This thesis describes the isolation and characterization of this organism, and lays the foundation for future studies of its metabolism and genetics, including aspects of nitrogen and carbon fixation; as well as the synthesis, regulation and stability of cell wall and cell membrane components under highly saline and alkaline conditions. vi TABLE OF CONTENTS Thesis Signature Page Title Page ii Acknowledgements iii Abstract v Table of Contents vi List of Tables vii List of Figures viii Introduction 1 Materials and Methods 16 Results 23 Discussion 39 Literature Cited 49 Curriculum Vita 58 vii LIST OF TABLES Table 1: Absorption spectra of various bacteriochlorophyll 9 molecules in vivo Table 2: The uncorrected percent similarity of 16S rDNA sequences 27 of various Purple Sulfur Bacteria, reference species and strain MLS1 Table 3: Cell yields of Ectothiorhodospira strain MLS1 with organic 31 components photoassimilated as carbon source and electron donor Table 4: Comparison of morphological and physiological 41 characteristics of Ectothiorhodospira strain MLS1 to Ectothiorhodospiraceae type strains described in Bergey's Manual of Systematic Bacteriology as well as E. haioaikaliphila (BN 9903) Table 5: Photosynthetic electron donors and carbon sources used by 46 species of the family Ectothiorhodospiraceae viii LIST OF FIGURES Figure 1: Absorption spectrum of whole cell samples from the Mono 23 Lake Shore primary enrichment Figure 2: Agar streak plate of the MLS enrichment showing the 24 presence of the two distinct colony types Figure 3: Whole cell absorption spectra of the phototrophic 24 bacterium and the unpigmented contaminant Figure 4: Growth of strain MLS1 in DSIC-II media agar plate and 25 liquid culture Figure 5: PCR amplification of 16S rDNA from strain MLS1 26 Figure 6: Alignment of strain MLS1 partial 16S rDNA with 28 comparable regions from related organisms shown in Table 2 Figure 7: Phylogenetic tree of strain MLS1 from Mono Lake to other 29 members of the genera Ectothiorhodospira and Haiorhodospira Figure 8: Phase contrast micrograph of Ectothiorhodospira strain 29 MLS1 Figure 9: Absorption spectra of intact cells and methanol:acetone 30 extracts of Ectothiorhodospira strain MLS1 ix Figure 10A: Effect of NaCl concentration on the growth of 32 Ectothiorhodospira strain MLS1 Figure 10B: Photo showing the color and relative densities of 33 Ectothiorhodospira strain MLS1 cultures from the salinity optimization experiments shown in Figure 10A Figure 11A: Effect of pH on the growth of Ectothiorhodospira strain 34 MLS1 Figure 11 B: Photo showing the color and relative densities of 34 Ectothiorhodospira strain MLS1 cultures from the pH optimization experiments shown in Figure 11A Figure 12: Relationship between total cellular protein (f,lg/ml) and 35 absorbency of cultures at 600nm Figure 13: Comparison of total cell protein content of 36 Ectothiorhodospira strain MLS1 under various culture conditions Figure 14: Growth curve of Ectothiorhodospira strain MLS1 using 38 medium DSIC-II (9mM NH4Cl) and medium EM-II (9mM NH4Cl), and medium DSIC-II with glutamine (14mM) 1 INTRODUCTION Life in Extreme Environments: An Overview Life flourishes on Earth in an incredibly wide range of environments, from high-salt deserts to volcanoes to polar ice. Yet it was only about 30 years ago when scientists began to discover that microbial life was not restricted to a limited range of environments, defined by a relatively narrow range of environmental factors (temperature, pH, water availability, and nutrient source). It has clear that there is no environment on the planet that contains eukaryotic organisms but is devoid of bacteria. However, there are numerous bacterial habitats that are devoid of eukaryotic organisms. From a eukaryotic (human) perspective, these latter environments are classified as extreme. The noted microbiologist Thomas Brock defined an extreme environment as one in which the physical or nutritional conditions present deviate radically from those same conditions normally associated with the taxonomic group in question (7). This definition is unique in characterizing an extremophile, as it is dependent not solely upon the extreme nature of the environment. More specifically, it also allows for defining extreme as deviating from the normal conditions within which the relatives of an organism are normally found. These habitats include extremes of 0 temperature (e.g. > 80 ( to < O°C), pH (> 10 to < 0), salinity (3 - 15% NaCl), high pressure (400-1110 atm), low water activity (aw < 0.800) and/or combinations of these parameters (30, 42, 56, 59, 65, 73). Although these conditions are extreme from the perspective of most higher animals, they are usually absolutely essential for the survival of a given organism. For example, the hyperthermophilic Archaean Pyrodictium has an optimal growth temperature of 105°(, with a growth range between 82° 0 and 110 ( (68, 69). At temperatures lower than 70°(, metabolic activity ceases and the cells die due to the denaturation of critical metabolic 2 enzymes and the instability of the plasma membrane. A seemingly hospitable environment is actually extreme for Pyrodictium. The study of microbial life forms and the extreme environments in which they exist is providing new insights into how organisms have evolved and adapted to diverse environments. This knowledge will provide the basis to understand not only how life originated and evolved on Earth, but also how life may thrive on other planets. In addition, the development of new technologies and experimental approaches in microbiology has
Load more

Recommended publications
  • Int J Syst Evol Microbiol 67 1
    Author version : International Journal of Systematic and Evolutionary Microbiology, vol.67(6); 2017; 1949-1956 Imhoffiella gen. nov.. a marine phototrophic member of family Chromatiaceae including the description of Imhoffiella purpurea sp. nov. and the reclassification of Thiorhodococcus bheemlicus Anil Kumar et al. 2007 as Imhoffiella bheemlica comb. nov. Nupur1, Mohit Kumar Saini1, Pradeep Kumar Singh1, Suresh Korpole1, Naga Radha Srinivas Tanuku2, Shinichi Takaichi3 and Anil Kumar Pinnaka1* 1Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, INDIA 2CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam-530017, INDIA 3Nippon Medical School, Department of Biology, Kyonan-cho, Musashino 180-0023, Japan Address for correspondence* Dr. P. Anil Kumar Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh – 160 036, INDIA Email: [email protected] Telephone: 00-91-172-6665170 Running title Imhoffiella purpurea sp. nov. Subject category New taxa (Gammaproteobacteria) The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain AK35T is HF562219. A coccoid-shaped phototrophic purple sulfur bacterium was isolated from a coastal surface water sample collected from Visakhapatnam, India. Strain AK35T was Gram-negative, motile, purple colored, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16:0, C18:1 T 7c and C16:1 7c and/or iso-C15:0 2OH (Summed feature 3) were identified.
    [Show full text]
  • Coupled Reductive and Oxidative Sulfur Cycling in the Phototrophic Plate of a Meromictic Lake T
    Geobiology (2014), 12, 451–468 DOI: 10.1111/gbi.12092 Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake T. L. HAMILTON,1 R. J. BOVEE,2 V. THIEL,3 S. R. SATTIN,2 W. MOHR,2 I. SCHAPERDOTH,1 K. VOGL,3 W. P. GILHOOLY III,4 T. W. LYONS,5 L. P. TOMSHO,3 S. C. SCHUSTER,3,6 J. OVERMANN,7 D. A. BRYANT,3,6,8 A. PEARSON2 AND J. L. MACALADY1 1Department of Geosciences, Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA 2Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 3Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 4Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA 6Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Nanyang, Singapore 7Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany 8Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA ABSTRACT Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacte- ria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary pro- duction in Mahoney Lake. Here, we present metagenomic data from this phototrophic plate – including the genome of the major PSB, as obtained from both a highly enriched culture and from the metagenomic data – as well as evidence for multiple other taxa that contribute to the oxidative sulfur cycle and to sulfate reduction.
    [Show full text]
  • This Article Was Published in an Elsevier Journal. the Attached Copy
    This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and education use, including for instruction at the author’s institution, sharing with colleagues and providing to institution administration. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 72 (2008) 1396–1414 www.elsevier.com/locate/gca Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation Jochen J. Brocks a,*, Philippe Schaeffer b a Research School of Earth Sciences and Centre for Macroevolution and Macroecology, The Australian National University, Canberra, ACT 0200, Australia b Laboratoire de Ge´ochimie Bio-organique, CNRS UMR 7177, Ecole Europe´enne de Chimie, Polyme`res et Mate´riaux, 25 rue Becquerel, 67200 Strasbourg, France Received 20 June 2007; accepted in revised form 12 December 2007; available online 23 December 2007 Abstract Carbonates of the 1640 million years (Ma) old Barney Creek Formation (BCF), McArthur Basin, Australia, contain more than 22 different C40 carotenoid derivatives including lycopane, c-carotane, b-carotane, chlorobactane, isorenieratane, b-iso- renieratane, renieratane, b-renierapurpurane, renierapurpurane and the monoaromatic carotenoid okenane.
    [Show full text]
  • Complete Genome Sequence of Strain BW-2, a Magnetotactic
    Complete Genome Sequence of Strain BW-2, a Magnetotactic Gammaproteobacterium in the Family Ectothiorhodospiraceae , Isolated from a Brackish Spring in Death Valley, California Corey Geurink, Christopher Lefèvre, Caroline Monteil, Viviana Morillo-Lopez, Fernanda Abreu, Dennis Bazylinski, Denis Trubitsyn To cite this version: Corey Geurink, Christopher Lefèvre, Caroline Monteil, Viviana Morillo-Lopez, Fernanda Abreu, et al.. Complete Genome Sequence of Strain BW-2, a Magnetotactic Gammaproteobacterium in the Family Ectothiorhodospiraceae , Isolated from a Brackish Spring in Death Valley, California. Microbiology Resource Announcements, American Society for Microbiology, 2020, 9 (1), 10.1128/mra.01144-19. cea-02462734 HAL Id: cea-02462734 https://hal-cea.archives-ouvertes.fr/cea-02462734 Submitted on 3 Feb 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. GENOME SEQUENCES crossm Complete Genome Sequence of Strain BW-2, a Magnetotactic Gammaproteobacterium in the Family Ectothiorhodospiraceae, Downloaded from Isolated from a Brackish Spring in Death
    [Show full text]
  • Menaquinone As Pool Quinone in a Purple Bacterium
    Menaquinone as pool quinone in a purple bacterium Barbara Schoepp-Cotheneta,1, Cle´ ment Lieutauda, Frauke Baymanna, Andre´ Verme´ gliob, Thorsten Friedrichc, David M. Kramerd, and Wolfgang Nitschkea aLaboratoire de Bioe´nerge´tique et Inge´nierie des Prote´ines, Unite´Propre de Recherche 9036, Institut Fe´de´ ratif de Recherche 88, Centre National de la Recherche Scientifique, F-13402 Marseille Cedex 20, France; bLaboratoire de Bioe´nerge´tique Cellulaire, Unite´Mixte de Recherche 163, Centre National de la Recherche Scientifique–Commissariat a`l’E´ nergie Atomique, Universite´ delaMe´ diterrane´e–Commissariat a`l’E´ nergie Atomique 1000, Commissariat a` l’E´ nergie Atomique Cadarache, Direction des Sciences du Vivant, De´partement d’Ecophysiologie Ve´ge´ tale et Microbiologie, F-13108 Saint Paul Lez Durance Cedex, France; cInstitut fu¨r Organische Chemie und Biochemie, Albert-Ludwigs-Universita¨t Freiburg, Albertstr. 21, D-79104 Freiburg, Germany; and dInstitute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340 Edited by Pierre A. Joliot, Institut de Biologie Physico-Chimique, Paris, France, and approved March 31, 2009 (received for review December 23, 2008) Purple bacteria have thus far been considered to operate light- types of pool-quinones, such as ubi-, plasto-, mena-, rhodo-, driven cyclic electron transfer chains containing ubiquinone (UQ) as caldariella- or sulfolobus-quinones (to cite only the best-studied liposoluble electron and proton carrier. We show that in the purple cases) have been identified so far individually in different species ␥-proteobacterium Halorhodospira halophila, menaquinone-8 or coexisting in single organisms (2–4). (MK-8) is the dominant quinone component and that it operates in Menaquinone (MK) is the most widely distributed quinone on the QB-site of the photosynthetic reaction center (RC).
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,501,463 B2 Cox Et Al
    USOO85O1463B2 (12) United States Patent (10) Patent No.: US 8,501,463 B2 Cox et al. (45) Date of Patent: Aug. 6, 2013 (54) ANAEROBC PRODUCTION OF HYDROGEN (56) References Cited AND OTHER CHEMICAL PRODUCTS U.S. PATENT DOCUMENTS (75) Inventors: Marion E. Cox, Morgan Hill, CA (US); 5,350,685 A 9/1994 Taguchi et al. Laura M. Nondorf, Morgan Hill, CA 5,464,539 A 11/1995 Ueno et al. 6,090,266 A 7/2000 Roychowdhury (US); Steven M. Cox, Morgan Hill, CA 6,251,643 B1 6/2001 Hansen et al. (US) 6,299,774 B1 * 10/2001 Ainsworth et al. ........... 210,603 6,342,378 B1 1/2002 Zhang et al. (73) Assignee: Anaerobe Systems, Morgan Hill, CA 6,569,332 B2 * 5/2003 Ainsworth et al. ........... 210,603 2004/0050778 A1 3/2004 Noike et al. (US) 2004/O115782 A1 6/2004 Paterek (*) Notice: Subject to any disclaimer, the term of this FOREIGN PATENT DOCUMENTS patent is extended or adjusted under 35 WO WO-2006-119052 A2 11/2006 U.S.C. 154(b) by 1347 days. OTHER PUBLICATIONS (21) Appl. No.: 11/912,881 Liu et al., 2004. Effects of Culture and Medium Conditions on Hydro gen Production from Starch Using Anaerobic Bacteria. Journal of (22) PCT Fled: Apr. 27, 2006 Bioscience and Bioengineering, vol. 98, No. 4, pp. 251-256.* Zhang et al., Distributed Computer Control of Penicillin Fermenta (86) PCT NO.: PCT/US2OO6/O16332 tion Industrial Production. Proceedings of the IEEE International Conference on Industrial Technology, 1996, pp. 52-56.* S371 (c)(1), New Brunswick, an eppenforf Company, pp.
    [Show full text]
  • Photosynthesis Is Widely Distributed Among Proteobacteria As Demonstrated by the Phylogeny of Puflm Reaction Center Proteins
    fmicb-08-02679 January 20, 2018 Time: 16:46 # 1 ORIGINAL RESEARCH published: 23 January 2018 doi: 10.3389/fmicb.2017.02679 Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Johannes F. Imhoff1*, Tanja Rahn1, Sven Künzel2 and Sven C. Neulinger3 1 Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 Max Planck Institute for Evolutionary Biology, Plön, Germany, 3 omics2view.consulting GbR, Kiel, Germany Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Edited by: Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the Marina G. Kalyuzhanaya, phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria San Diego State University, United States employing this photosystem in nature. Almost complete pufLM gene sequences and Reviewed by: the derived protein sequences from 152 type strains and 45 additional strains of Nikolai Ravin, phototrophic Proteobacteria employing photosystem II were compared. The results Research Center for Biotechnology (RAS), Russia give interesting and comprehensive insights into the phylogeny of the photosynthetic Ivan A. Berg, apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as Universität Münster, Germany major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from *Correspondence: Caulobacterales (Brevundimonas subvibrioides).
    [Show full text]
  • Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2010 Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi South Dakota School of Mines and Technology Shariff Osman Lawrence Berkeley National Laboratory Ravi K. Kukkadapu Pacific Northwest National Laboratory, [email protected] Mark Engelhard Pacific Northwest National Laboratory Parag A. Vaishampayan California Institute of Technology See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub Part of the Bioresource and Agricultural Engineering Commons Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi K.; Engelhard, Mark; Vaishampayan, Parag A.; Andersen, Gary L.; and Sani, Rajesh K., "Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota" (2010). US Department of Energy Publications. 170. https://digitalcommons.unl.edu/usdoepub/170 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Gurdeep Rastogi, Shariff Osman, Ravi K. Kukkadapu, Mark Engelhard, Parag A. Vaishampayan, Gary L. Andersen, and Rajesh K. Sani This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdoepub/170 Microb Ecol (2010) 60:539–550 DOI 10.1007/s00248-010-9657-y SOIL MICROBIOLOGY Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi & Shariff Osman & Ravi Kukkadapu & Mark Engelhard & Parag A.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]
  • Bergey's Manual Of
    BERGEY’S MANUALா OF Systematic Bacteriology Second Edition Volume Two The Proteobacteria Part B The Gammaproteobacteria BERGEY’S MANUALா OF Systematic Bacteriology Second Edition Volume Two The Proteobacteria Part B The Gammaproteobacteria Don J. Brenner Noel R. Krieg James T. Staley EDITORS, VOLUME TWO George M. Garrity EDITOR-IN-CHIEF EDITORIAL BOARD James T. Staley, Chairman, David R. Boone, Vice Chairman, Don J. Brenner, Paul De Vos, George M. Garrity, Michael Goodfellow, Noel R. Krieg, Fred A. Rainey, Karl-Heinz Schleifer WITH CONTRIBUTIONS FROM 339 COLLEAGUES George M. Garrity, Sc.D. Bergey’s Manual Trust Department of Microbiology and Molecular Genetics Michigan State University East Lansing, MI 48824-4320 USA Library of Congress Cataloging-in-Publication Data TO COME This volume is dedicated to our colleagues, David R. Boone, Don J. Brenner, Richard W. Castenholz, and Noel R. Krieg, who retired from the Board of Trustees of Bergey’s Manual Trust as this edition was in preparation. We deeply appreciate their efforts as editors and authors; they have devoted their time and many years in helping the Trust meet its objectives. EDITORIAL BOARD AND TRUSTEES OF BERGEY’S MANUAL TRUST James T. Staley, Chairman David R. Boone, Vice Chairman George M. Garrity Paul De Vos Michael Goodfellow Fred A. Rainey Karl-Heinz Schleifer Don J. Brenner, Emeritus Richard W. Castenholz, Emeritus John G. Holt, Emeritus Noel R. Krieg, Emeritus John Liston, Emeritus James W. Moulder, Emeritus R.G.E. Murray, Emeritus Charles F. Niven, Jr., Emeritus Norbert Pfennig, Emeritus Peter H.A. Sneath, Emeritus Joseph G. Tully, Emeritus Stanley T.
    [Show full text]
  • Arhodomonas Aquaeolei Gen
    INTERNATIONAL JOURNAL OF SYSTEMATICBACTERIOU)GY, July 1993, p. 514-520 Vol. 43, No. 3 oO20-7713/93/030514-07$02.oO/O Copyright 0 1993, International Union of Microbiological Societies Arhodomonas aquaeolei gen. nov., sp. nov., an Aerobic, Halophilic Bacterium Isolated from a Subterranean Brine JON P. ADKINS,l MICHAEL T. MADIGAN,2 LINDA MANDELCO,, CARL R. WOESE,, AND RALPH S. TANNER'* Department of Botany and Microbiology, University of Oklahoma? Norman, Oklahoma 73019'; Department of Microbwlogy9 Southern Illinois University, Carbondale, Illinois 629012; and Department of Microbiology, University of Illinois, Urbana, Illinois 61801 Arhodomonas uquueolei gen. nov., sp. nov., isolated from a petroleum reservoir production fluid, is described. The single isolate was an obligately halophilic, aerobic, gram-negative, oval rod-shaped bacterium that was actively motile by means of a single polar flagellum. It was catalase and oxidase positive. The isolate had a specific requirement for NaCI; growth occurred at NaCI concentrations between 6 and 20%, and optimal growth occurred in the presence of 15% NaCI. This species metabolized primarily organic acids and required biotin for growth. The name Arhodomonas is proposed for the new genus, which was placed in the gamma subclass of the Proteobactek on the basis of the results of a 16s rRNA sequence analysis. Although A. uquaeohi is most closely related to purple sulfur bacteria (the genera Ectothwrhodospiru and Chromatiurn),it is not a phototrophic microorganism, which is consistent with its isolation from a subterranean environment. The major components of its cellular fatty acids were C16:., Cis:., CI9:., C16:1,and Clsz0 acids. The DNA base composition of the type strain is 67 mol% G+C.
    [Show full text]
  • Microbiology of Lonar Lake and Other Soda Lakes
    The ISME Journal (2013) 7, 468–476 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej MINI REVIEW Microbiology of Lonar Lake and other soda lakes Chakkiath Paul Antony1, Deepak Kumaresan2, Sindy Hunger3, Harold L Drake3, J Colin Murrell4 and Yogesh S Shouche1 1Microbial Culture Collection, National Centre for Cell Science, Pune, India; 2CSIRO Marine and Atmospheric Research, Hobart, TAS, Australia; 3Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany and 4School of Environmental Sciences, University of East Anglia, Norwich, UK Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalk- aliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases.
    [Show full text]