DOCSLIB.ORG

1 Bridging 200 Years of Bacterial Classification

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1 Bridging 200 Years of Bacterial Classification 1 Bridging 200 Years of Bacterial Classification Ramon Rosselló-Móra1 and Erko Stackebrandt2,* 1Grup de Microbiologia Marina, Department Animal and Microbial Diversity, IMEDEA (CSIC-UIB), Esporles, Spain; 2Kneitlingen, OT Ampleben, Germany Introduction bacterial names and classification systems. The first was the establishment of the Approved List The history of bacterial systematics reflects of Bacterial Names (Skerman et al., 1980) that scientific progress in which approaches (often brought order into the huge number of syn- developed in non-biological disciplines) were onyms based on obscure species descriptions; adopted to improve the accuracy of bacterial the second was the perception that proper classi- taxonomy and to develop comprehensible rela- fication needed to be based upon phylogenetic tionships. What started two centuries ago with a relationships. Within a short period of 20 blurred vision of the simplest properties of the years the tree of life began to unfold, and what bacterial cell became more focused once pure originally was founded on a single evolutionary cultures were achievable. At an amazing speed, conservative gene has now been extended to their existence as both harmful pathogens for genome sequences. Moreover, the era in which humans, plants and animals and as beneficial pure cultures were needed to assess phylogenetic partners in agriculture, food and industrial ap- novelty has been extended to the direct applica- plications was disclosed. Microbiology as a scien- tion of metagenome and microbiome studies to tific discipline in its own right was established, environmental samples. As a result, the ‘trad- although the historical connection to botany was itional’ bacteriologists are confronted with the still recognizable until recently. In parallel with interest of ‘molecular systematists’ in giving the enormous avalanche of strains, names and names to as yet uncultured organisms and even accompanying data already generated at the to genomes or fragments thereof. No doubt, dawn of microbiology, attempts were made to without a mutual understanding of the ration- understand the origin of bacteria, and to order ale and purpose of naming the individual en- them into a system that depicted the relationships tities (from genes to cultured cells) confusion is among themselves and to other living organ- bound to occur, especially if different entities of isms. A large number of systems were outlined a given organism are named differently. This with hardly any of them being identical to another. chapter will briefly take a historical view of the It was not until far into the 20th century that major steps in bacterial systematics leading to two major events occurred that would change the first reconciliation workshop in 1987 and a our perception of how to reject the plethora of re-evaluation of the species concept in 2002. *[email protected] © CAB International 2021. Trends in the Systematics of Bacteria and Fungi (eds. P. Bridge, D. Smith and E. Stackebrandt) 1 2 R. Rosselló-Móra and E. Stackebrandt New challenges and concepts developed since field. But this era also saw the exploration into then will be outlined. other scientific fields, such as immunology, chemotherapy, physiology, industrial microbiol- ogy, biochemistry and the study of metabolisms, The Historical Perspective leading to a rapid growth in knowledge about the properties of microorganisms and their inter- The changing consideration of bacterial actions with biotic and abiotic matter. taxonomic assessment In the second half of the 19th century the de- position and exchange of microbial cultures; the The early era organization of international conferences; and the accessibility of scientific literature was limited, Microorganisms became visible by means of the and it is not surprising that individual systematists introduction of Antony van Leeuwenhoek’s generated a plethora of systems. Migula (1900) microscope in the mid-17th century. He and Lazza- compared about 30 such systems, published be- ro Spallanzani objected to the idea of spontaneous tween 1836 and 1894. At the dawn of microbiol- generation of microorganisms, and paved the way ogy, and even later, the same microorganism was for the future development of the science of micro- given different names as individual researchers biology. It took about another 100 years before the based their taxonomy on different properties. It first report on classification and characterization was not until 1980 that the Approved List of Bac- of microorganisms was attempted (Müller, 1786). terial Names (Skerman et al., 1980) brought no- Another century of optical and instrumental im- menclatural order into bacteriology by starting a provement passed before the name ‘Bacterium’ as a new date for bacterial nomenclature. The tens of genus was introduced as a scientific word by Chris- thousands of names for bacterial species were re- tian Gottfried Ehrenberg (1838). As Ehrenberg duced to about 2500 names that could be linked stated: ‘eine Milchstrasse der kleinsten Organisa- unambiguously to a previously defined name of a tion geht duch die Gattungen Monas, Vibrio, Bac- bacterial species. Nevertheless, despite the meth- terium…’ (‘a Milky Way of the smallest organization odological shortcomings of taxon descriptions, runs through the genera Monas, Vibrio, Bacter- the early 19th century must be considered a period ium…’). However, while at that time their occur- of great scientific achievement and accurate ob- rence and relationships in different niches became servations, as some of the names given to bacteria apparent to the early microbiologists, neither their with particular morphologies in the first half of ecological function nor their mutual relationships the 19th century (e.g. Spirillum [Ehrenberg, revealed themselves to the observer. 1835], Spirochaeta [Ehrenberg, 1835] and Sarcina It is a part of human nature to arrange sub- [Goodsir, 1842]) were recognized as valid and in- jects into categories, no matter how small the cluded in the Approved List. number and how difficult the selection criteria. To recognize the historic development of Being mostly botanist by education is not surpris- species characterization and the changes in affili- ing that, in the absence of facts about their phyl- ating genera to higher taxa we use the fate of Vib- ogeny, the nature of bacteria (based on nothing rio cholerae as an example, starting from the first more than basic morphological descriptions) description by Filipo Pacini (1854) through a ser- could not be properly evaluated by these early sys- ies of progress reports as laid down in Bergey’s tematists. The apparent similarity of mainly uni- Manual of Determinative Bacteriology and later cellular forms and separation by fission allowed of Bergey’s Manual of Systematic Bacteriology. the early microbial systematists to deduce that Almost any other taxon described before the late bacteria derived from animals (van Leeuwen- 20th century was prone to the same fate as the hoek, Müller, Ehrenberg), and later from fungi, genus Vibrio and its type species V. cholerae. classifying them as Schizophytae (Cohn, 1872), a system in which bacteria were placed together A witness of scientific progress: Bergey’s with ‘Spaltalgen’ (today named cyanobacteria). Manual of Determinative Bacteriology This early period which Paul de Kruif (1926) characterizes so well in his famous novel Microbe About 20 years after the publication of Ehrenberg Hunters is dominated by discoveries in the medical (1832) a Vibrio-shaped bacterium was deduced Phase 4: to present In silico genome analysis of relationships; genome-based phylogeny; rRNA gene, housekeeping genes and genome ecotype concept; sequences; MLST and MLSA; MALDI-TOF, DNA patterns; rapid molecular identification tools; FISH-probes; -omics; integrated databases 2nd reconciliation workshop Bridging 200 Years of Bacterial Classification ofBacterial Years Bridging 200 1st reconciliation workshop; Phase 3: mid-1950s–mid-1980s polyphasic taxonomy; commercial kits; Numerical taxonomy; chemotaxonomy; DNA-DNA and rRNA gene sequence- DNA-rRNA reassociation; mol% G+C of DNA; (evolution/objective)-based phylogeny rRNA gene cataloguing; anaerobic techniques Phase 2: until mid-1950s Subjective classification into ranks Ecology; biochemistry; genetics; serology; based on individual observations; immunology unravelling the high diversity and niches of microorganisms Phase 1: around 1880–1900 Around 1850: considering microorganisms as Medical microbiology; first species description; pathogenic agents; the early champions of culture observation; physiology microbiology Early 1600s: Beginning of microscopy Fig. 1.1. Development of taxonomic approaches through different historical phases. MLST: Multilocus Sequence Typing; FISH: Fluorescent in situ Hybridization. 3 4 R. Rosselló-Móra and E. Stackebrandt as the most likely causative agent of cholera dis- the turn of the 19th century. Although DNA was ease and was named V. cholerae by Pacini (1854), discovered around 1860, bacterial transform- although for several decades Robert Koch was ation experiments were published in the 1920s, listed as the discoverer of this bacterium. For and chromosomes were identified as the cellular some of the reasons indicated above, strains of structures responsible for heredity, the structure this species or similar organisms were named of DNA had still not been deciphered and genet- (among others) Bacillus cholerae-asiaticae (Pacini, ics was in its infancy. The absence of a clearly
Load more

Recommended publications
  • Introduction to Bacteriology and Bacterial Structure/Function
    INTRODUCTION TO BACTERIOLOGY AND BACTERIAL STRUCTURE/FUNCTION LEARNING OBJECTIVES To describe historical landmarks of medical microbiology To describe Koch’s Postulates To describe the characteristic structures and chemical nature of cellular constituents that distinguish eukaryotic and prokaryotic cells To describe chemical, structural, and functional components of the bacterial cytoplasmic and outer membranes, cell wall and surface appendages To name the general structures, and polymers that make up bacterial cell walls To explain the differences between gram negative and gram positive cells To describe the chemical composition, function and serological classification as H antigen of bacterial flagella and how they differ from flagella of eucaryotic cells To describe the chemical composition and function of pili To explain the unique chemical composition of bacterial spores To list medically relevant bacteria that form spores To explain the function of spores in terms of chemical and heat resistance To describe characteristics of different types of membrane transport To describe the exact cellular location and serological classification as O antigen of Lipopolysaccharide (LPS) To explain how the structure of LPS confers antigenic specificity and toxicity To describe the exact cellular location of Lipid A To explain the term endotoxin in terms of its chemical composition and location in bacterial cells INTRODUCTION TO BACTERIOLOGY 1. Two main threads in the history of bacteriology: 1) the natural history of bacteria and 2) the contagious nature of infectious diseases, were united in the latter half of the 19th century. During that period many of the bacteria that cause human disease were identified and characterized. 2. Individual bacteria were first observed microscopically by Antony van Leeuwenhoek at the end of the 17th century.
    [Show full text]
  • 1 Molecular Analysis of Honey Bee Foraging Ecology Dissertation
    Molecular analysis of honey bee foraging ecology Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Rodney Trey Richardson Graduate Program in Entomology The Ohio State University 2018 Dissertation Committee Professor Reed Johnson, Advisor Professor Mary Gardiner Professor John Christman Professor Roman Lanno 1 Copyrighted by Rodney Trey Richardson 2018 2 Abstract While numerous factors currently impact the health of honey bees and other pollinating Hymenoptera, poor floral resource availability due to habitat loss and land conversion is thought to be important. This issue is particularly salient in the upper Midwest, a location which harbors approximately 60 percent of the US honey bee colonies each summer for honey production. This region has experienced a dramatic expansion in the area devoted to crop production over the past decade. Consequently, understanding how changes to landscape composition affect the diversity, quality and quantity of available floral resources has become an important research goal. Here, I developed molecular methods for the identification of bee-collected pollen by adapting and improving upon the existing amplicon sequencing infrastructure used for microbial community ecology. In thoroughly benchmarking our procedures, I show that a simple and cost-effective three-step PCR-based library preparation protocol in combination with Metaxa2-based hierarchical classification yields an accurate and highly quantitative pollen metabarcoding approach when applied across multiple plant markers. In Chapter 1, I conducted one of the first ever proof-of-concept studies applying amplicon sequencing, or metabarcoding, to the identification of bee-collected pollen.
    [Show full text]
  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
    [Show full text]
  • Open Thweattetd1.Pdf
    The Pennsylvania State University The Graduate School CHARACTERIZATION OF PIGMENT BIOSYNTHESIS AND LIGHT-HARVESTING COMPLEXES OF SELECTED ANOXYGENIC PHOTOTROPHIC BACTERIA A Dissertation in Biochemistry, Microbiology, and Molecular Biology and Astrobiology by Jennifer L. Thweatt 2019 Jennifer L. Thweatt Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2019 ii The dissertation of Jennifer L. Thweatt was reviewed and approved* by the following: Donald A. Bryant Ernest C. Pollard Professor in Biotechnology and Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Squire J. Booker Howard Hughes Medical Investigator Professor of Chemistry and Professor of Biochemistry and Molecular Biology Eberly Distinguished Chair in Science John H. Golbeck Professor of Biochemistry and Biophysics Professor of Chemistry Jennifer L. Macalady Associate Professor of Geosciences Timothy I. Miyashiro Assistant Professor of Biochemistry and Molecular Biology Wendy Hanna-Rose Professor of Biochemistry and Molecular Biology Department Head, Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT This dissertation describes work on pigment biosynthesis and the light-harvesting apparatus of two classes of anoxygenic phototrophic bacteria, namely the green bacteria and a newly isolated purple sulfur bacterium. Green bacteria are introduced in Chapter 1 and include chlorophototrophic members of the phyla Chlorobi, Chloroflexi, and Acidobacteria. The green bacteria are defined by their use of chlorosomes for light harvesting. Chlorosomes contain thousands of unique chlorin molecules, known as bacteriochlorophyll (BChl) c, d, e, or f, which are arranged in supramolecular aggregates. Additionally, all green bacteria can synthesize BChl a, the and green members of the phyla Chlorobi and Acidobacteria can synthesize chlorophyll (Chl) a.
    [Show full text]
  • Genetic Markers and Plant Genetic Resource Management P
    NCRPIS Publications and Papers North Central Regional Plant Introduction Station 1995 Genetic Markers and Plant Genetic Resource Management P. K. Bretting United States Department of Agriculture Mark P. Widrlechner Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/ncrpis_pubs Part of the Agricultural Science Commons, Agriculture Commons, and the Plant Breeding and Genetics Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ ncrpis_pubs/75. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Book Chapter is brought to you for free and open access by the North Central Regional Plant Introduction Station at Iowa State University Digital Repository. It has been accepted for inclusion in NCRPIS Publications and Papers by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Plant Breeding Reviews, Volume 13 Edited by Jules Janick © 1995 John Wiley & Sons, Inc. ISBN: 978-0-471-57343-2 12 P. K. BRETTING AND M. P. WIDRLECHNER C. Maintenance 1. Maintaining Trueness-to-Type a. Morphological Traits b. Secondary Metabolites c. Isozymes, Seed Proteins, and DNA Markers d. Comparative Studies e. Pollination Control Methods 2. Monitoring Shifts in Population Genetic Structure in Heterogeneous Germplasm a. Deviations from Random Mating b. Regeneration of Autogamous Species 3. Monitoring Genetic Shifts Caused by Differential Viability in Storage 4. Monitoring Genetic Shifts Caused by In Vitro Culture 5. Monitoring Germplasm Viability and Health D. Utilization 1. Developing Optimal Utilization Strategies from Genetic Marker Data 2.
    [Show full text]
  • Género Spirillum
    GÉNERO SPIRILLUM INTEGRANTES: CONDORI BAUTISTA ROBERTO CONDORI YUJRA MARUJA GARCIA CONDE ANAHI NINETH DOCENTE: Dr. JHON QUISBERT ARUQUIPA MATERIA: MICROBIOLOGIA CARRERA: MEDICINA “Conserva en tu hogar y ocupará tu lugar; el roedor vector de Spirillum puede enfermar del fiebre espirilar”. EL ALTO- BOLIVIA 2013 SINONIMIA O NOMBRES SPIRILLUM MINUS ALTERNATIVOS. AGENTE ETIOLÓGICO Esta enfermedad es conocida como: “Fiebre por mordedura de ratas” (FMR) oRBF DE LA FIEBRE POR (Feverfor Bite of Rats); en Japón se lo conoce como SODOKU(término MORDEDURA DE japonés donde 'so'' es rata y 'doku'' veneno ), es causada por Spirillum minus. Según otros datos se los RATA conoce como: mursu muris “SODUKU, enfermedad febril causada por espiroqueta Spironema (SODOKU) o Spirochaeta morsus murisy Fiebre espirilar. El agente etiológicoprincipalment e es conocida con el nombre Spirillum minus, pero también como Spirillum morsus muris, Spirochaeta muris, Spirochaeta morsus minus, Spirilla morsus minus, Spirillum minor (aunque mal dicha). 1 AGRADECIMENTO Y DEDICATORIA. A NUESTROS PADRES POR SU APOYO INCONDICIONAL. A NUESTRO QUERIDO DOCENTE JHON QUISBERT POR INCENTIVAR LA INVESTIGACION. Y POR SOBRE TODO A DIOS POR DARNOS EL CONOCIMIENTO Y LA SABIDURIA. 2 INDICE INDICE…………………………………………………………………………………………pag.3/4 I. INTRODUCCIÓN…………………………………………………………………….pag.5 II. ANTECEDENTES…………………………………………………………………….pag.6 III. JUSTIFICACIÓN……………………………………………………………………..pag.7 IV. OBJETIVOS………………………………………………………………………………. A. GENERAL…………………………………………………………………………… B. ESPECÍFICOS V. MARCO
    [Show full text]
  • Bee Pollen Diet Alters the Bacterial Flora and Antimicrobial Peptides in the Oral Cavities of Mice
    foods Article Bee Pollen Diet Alters the Bacterial Flora and Antimicrobial Peptides in the Oral Cavities of Mice Ariuntsetseg Khurelchuluun 1,2,† , Osamu Uehara 3,† , Durga Paudel 1 , Tetsuro Morikawa 1, Yutaka Kawano 4 , Mashu Sakata 5, Hiroshi Shibata 5, Koki Yoshida 1 , Jun Sato 1, Hiroko Miura 3, Hiroki Nagayasu 2 and Yoshihiro Abiko 1,* 1 Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] (A.K.); [email protected] (D.P.); [email protected] (T.M.); [email protected] (K.Y.); [email protected] (J.S.) 2 Division of Oral and Maxillofacial Surgery, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] 3 Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] (O.U.); [email protected] (H.M.) 4 Institute of Preventive Medical Science, Health Sciences University of Hokkaido, Ainosato 2-5, Kita-ku, Sapporo, Hokkaido 002-8072, Japan; [email protected] 5 Belle Coeur Institute, Utsukushigaoka 5-9-10-30, Kiyota-ku, Sapporo, Hokkaido 004-0851, Japan; [email protected] (M.S.); [email protected] (H.S.) * Correspondence: [email protected]; Tel.: +81-133-23-1390 † Both authors contributed equally to this work.
    [Show full text]
  • United States Patent (19) 11 Patent Number: 5,348,854 Webster, Jr
    US00534.8854A United States Patent (19) 11 Patent Number: 5,348,854 Webster, Jr. 45) Date of Patent: Sep. 20, 1994 54 METHOD FORDETECTINGPROKARYOTIC vol. 10, No. 2, "Overview of Automation and Identifi ORGANISMS cation,” pp. 18-20, William J. Martin (1979). 76 Inventor: John A. Webster, Jr., 5 Kenmar Dr., American Society for Microbiology News, vol. 49, No. 2, Bldg. 5, Apt. 21, Billerica, Mass. "Impact of Modern Taxonomy on Microbiology,” Don 01821 J. Brenner. International Code of Nomenclature of Bacteria and 21) Appl. No.: 21,551 Selected Statutes... Bacteriological Code, 1976 Revi 22 Filed: Mar. 2, 1987 sions; ASM, Washington, D.C. (1975). Arnot et al., Mol. Biochem. Parasitol. 3:47-56 (1981). Related U.S. Application Data Dunn et al., Cell 12:23-36 (1977). Mattei et al., Chem. Absts, vol. 86, No. 19, p. 267, Ab 63) Continuation of Ser. No. 695,223, Jan. 25, 1985, aban doned, Continuation-in-part of Ser. No. 305,498, Sep. stract No. 1362(e) (1977). 25, 1981, Pat. No. 4,717,653. Moseley, S. L. et al., J. Infect. Dis. 142:892-898 (1980). Acore, R. U., Current Topics in Microbiology and Im 51 Int. Cl. ............................................... C12Q 1/68 munobiology 64:105-128 (1974), edited by Springer, 52 U.S. C. .......................................... 435/6; 435/34; New York. 435/172.1; 435/810; 436/504; 436/545; 436/501; 436/804 Boros et al., Nucl. Acids Res, 6:1817-1830 (1979). 58) Field of Search .................. 435/6, 34, 172.1, 810; Saillard, Colette, J. N. Bove, "Methods in Mycro 436/504, 543, 545, 801, 501; 535/695, 223, 78, plasma,’ vol.
    [Show full text]
  • Effects of Shade Stress on Morphophysiology and Rhizosphere Soil Bacterial Communities of Two Contrasting Shade-Tolerant Turfgrasses
    Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses Juanjuan Fu ( [email protected] ) Northwest Agriculture and Forestry University https://orcid.org/0000-0001-8178-6698 Yilan Luo Northwest A&F University Pengyue Sun Northwest A&F University Jinzhu Gao Northwest A&F University Donghao Zhao Northwest A&F University Peizhi Yang Northwest A&F University Tianming Hu Northwest A&F University Research article Keywords: Community structure and diversity, Rhizosphere bacteria, Shade stress, Shade tolerance, 16S rRNA gene sequencing Posted Date: June 13th, 2019 DOI: https://doi.org/10.21203/rs.2.10288/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/14 Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress inuences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade- intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP.
    [Show full text]
  • Characterizing the Diversity of Active Bacteria in Soil by Comprehensive Stable Isotope Probing of DNA and RNA 18 with H2 O Elizabeth A
    ORIGINAL RESEARCH Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA 18 with H2 O Elizabeth A. Rettedal1 & Volker S. Brozel€ 1,2 1Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota 57007 2Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0004, South Africa Keywords Abstract 18 Bacterial diversity, DNA, H2 O, RNA, SIP, soil. Current limitations in culture-based methods have lead to a reliance on cul- ture-independent approaches, based principally on the comparative analysis of Correspondence primary semantides such as ribosomal gene sequences. DNA can be remarkably Elizabeth A. Rettedal, Department of Biology stable in some environments, so its presence does not indicate live bacteria, but and Microbiology, South Dakota State extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of University, Brookings SD 57007. active cells. Stable isotope probing (SIP) involves the incorporation of heavy Tel: + 45 4525 2506; Fax: + 45 4593 2809; isotopes into newly synthesized nucleic acids, and can be used to separate newly E-mail: [email protected] 18 synthesized from existing DNA or rRNA. H2 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. Funding Information The aim of our work was to compare soil bacterial community composition as We thank our reviewers for their helpful revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented 18 comments and suggestions. This research with H2 O and after 38 days the DNA and RNA were co-extracted. Heavy was funded by SD00H296-081HG from the nucleic acids were separated out by CsCl and CsTFA density centrifugation.
    [Show full text]
  • Identification of Small Endogenous Viral Elements Within Host
    IDENTIFICATION OF SMALL ENDOGENOUS VIRAL ELEMENTS WITHIN HOST GENOMES by Edward C. Davis, Jr. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Computer Science Boise State University May 2016 c 2016 Edward C. Davis, Jr. ALL RIGHTS RESERVED BOISE STATE UNIVERSITY GRADUATE COLLEGE DEFENSE COMMITTEE AND FINAL READING APPROVALS of the thesis submitted by Edward C. Davis, Jr. Thesis Title: Identification of Small Endogenous Viral Elements within Host Genomes Date of Final Oral Examination: 04 March 2016 The following individuals read and discussed the thesis submitted by student Edward C. Davis, Jr., and they evaluated his presentation and response to questions during the final oral examination. They found that the student passed the final oral examination. Timothy Andersen, Ph.D. Chair, Supervisory Committee Amit Jain, Ph.D. Member, Supervisory Committee Gregory Hampikian, Ph.D. Member, Supervisory Committee The final reading approval of the thesis was granted by Timothy Andersen, Ph.D., Chair, Supervisory Committee. The thesis was approved for the Graduate College by John R. Pelton, Ph.D., Dean of the Graduate College. Dedicated to Elaina, Arianna, and Zora. iv ACKNOWLEDGMENTS The author wishes to express gratitude to the members of the supervisory com- mittee for providing guidance and patience. v ABSTRACT A parallel string matching software architecture has been developed (incorpo- rating several algorithms) to identify small genetic sequences in large genomes. En- dogenous viral elements (EVEs) are sequences originating in the genomes of viruses that have become integrated into the chromosomes of sperm or egg cells of infected hosts, and passed to subsequent generations.
    [Show full text]
  • Haeckel's 1866 Tree of Life and the Origin of Eukaryotes
    PUBLISHED: 26 JULY 2016 | ARTICLE NUMBER: 16114 | DOI: 10.1038/NMICROBIOL.2016.114 correspondence Haeckel’s 1866 tree of life and the origin of eukaryotes To the Editor — In their Letter describing were summarized under the domain an expanded version of the tree of life, Eukarya, which includes all eukaryotic Hug et al.1 refer to a key publication of micro- and macroorganisms (from amoebae Carl Woese and co-workers2, wherein a to humans). 16S rRNA-phylogenetic scheme of the In chapter 26 entitled ‘Phylogenetic domains Bacteria, Archaea and Eukarya is theses’, Haeckel3 re-interpreted and shown. However, the first three-kingdom supplemented Darwin’s evolutionary tree of life that included microorganisms deductions of 1859. With reference to the was depicted by Ernst Haeckel (pictured simplest protists (bacteria), which form the at around 26 years old) in his General root of his ‘oak tree’ (see Fig. 6 in ref. 5), Morphology of Organisms, a seminal book Haeckel3 concluded that “all organisms that was published one hundred and are the descendants of such autogenous fifty years ago3. Moneren”. Hence, according to this In his Origin of Species, Charles Darwin Haeckelian interpretation of the phylogeny refers to the Linnean two-kingdom of life, the Monera (that is, Bacteria and system, with ‘Animalia’ and ‘Vegetabilia’ Archaea)2 are the progenitors of all more as the only two branches of the living complex living beings on Earth. world. Haeckel3, who was also known This 150-year-old idea is consistent with as the German Darwin4, introduced a recent discoveries and genomic analyses that three-kingdom scheme in which, as a support an archaeal origin of eukaryotes1,8.
    [Show full text]