MICROBIOLOGY Fundamentals and Applications

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2 MICROBIOLOGY Fundamentals and Applications Seventh Revised and Enlarged Edition S. S. Purohit Ex-Head P. G. Department of Botany Dungar College, Bikaner AGROBIOS (INDIA)

3 Published by: AGROBIOS (INDIA) Agro House, Behind Nasrani Cinema Chopasani Road, Jodhpur Phone: , Fax: E. mail: Web Site: agrobiosindia.com Agrobios(India) All Rights Reserved, 2006 First Edition: 1985 Second Edition: 1988 Third Edition: 1990 Reprinted: Fourth Edition: 1993 Fifth Edition: 1994 Reprinted: Sixth Edition: 1997 Reprinted: Seventh Revised & Enlarged Edition: 2006 All rights reserved. No part of the book or part thereof, including the title of the book, be reprinted in any from or language without the written permission of the author and the publishers. The copyists shall be prosecuted. ISBN No.: Price: Rs / US$ Published by: Dr. Updesh Purohit for Agrobios (India), Jodhpur Lasertypeset at: Shriya Computers and Printers, Jodhpur Cover Design by: Reena Printed at: Shyam Printing Press, Jodhpur

4 PREFACE Microbes are the part of our lives in more ways than most understand. Microbe is a term for tiny creatures that individually are too small to be seen with the unaided eye. Microbes include bacteria, archaea, fungi and protists. Archaea are bacteria-like creatures that have some traits not found in any true bacteria. Protists include primitive algae, amoebas, slime molds and protozoa. Viruses are also major type of microbe, though there is a debate as to whether viruses can be considered living creatures or not. Microbiology is the branch of biology that deals mainly with the study of microscopic organisms (microbes). It is one of the most applied of all the biological sciences. Although microbiology did not exist as a true science before the latter part of 19 th century, humans have undoubtedly been practitioners of microbiology since prehistoric times. Knowledge gained in this field has lad to the development of many concepts, which in turn resulted in action. The science of microbiology is subdivided into a number of diverse fields: Bacteriology is the study of the bacteria, Virology the study of viruses, Protozoology the study of protozoans, Phycology the study of algae, and Mycology is the study of fungi. These fields centre around the kinds of organisms under study. Other fields of microbiology centre around where the microbes grow and have the most significant effects like medical microbiology, food microbiology, agriculture (including biofertilizers, biopesticides, etc.), waste treatment, industrial microbiology (fermentation technology, bioprocessing), etc. Advances in microbiology helped in understanding various aspects of microbes specially medical microbiology (immunology, seriology, antibiotics development, vaccines, gene therapy) and genetic engineering Scientific development in microbiology has played an important role in the process of enrichment of developed countries. Any country seeking to develop its economy has to give significant priority to various branches of microbiology. Biotechnology is defined as the applications of scientific and engineering principles to the processing of material by biological agents to provide goods and services. Recently a new branch microbial biotechnology has been developed. The microbes are applied at industrial level, they constitute bioindustry which include, on the one hand, industrial activities where biotechnologies can replace technologies normally or currently in use and, on the other hand, industrial activities where microbial biotechnologies play an important driving role. There are several areas in which these technologies are being used. The important are chemical industry, food industry (mass production of yeast, algae and bacteria with a view of providing proteins, amino acids, vitamins, and use of enzymes), agricultural productivity, pharmaceutical industry, environmental protection and abatement of pollution, etc. The other important branch of microbial biotechnology is microbial genetic engineering. The text-cum-reference book to meet precisely the felt need is an outcome of author s active involvement in teaching, research in the field of microbiology for over thirty years. I believe that this book will be very useful to the undergraduate and postgraduate students in microbiology, teachers in academic and technical institutions and those who are interested in the subject. The book is divided

5 into forty seven chapters and covers comprehensively the content of all courses in microbiology for undergraduate and post graduate students of Universities in the country. The chapters have been arranged in such a manner as to lead the students through the entire gamut of microbiology. There is always ample scope for improvement and the same is wide enough for all to give valuable suggestion and critical analysis for the improvement in the style and content of the book in next edition. I am thankful to Dr. Updesh Purohit, Agrobios (India) for publishing the present edition well in time. S. S. Purohit

6 CONTENTS 1. Microbiology: Introduction and History... 1 Introduction... 1 Microbes Influencing Our Lives... 1 History of Microbiology... 3 Observing Microbes in Early Period... 3 Modern Age of Microbiology... 7 Louis Paustre: A Founding Father... 7 John Tyndall and Tyndallization... 9 Robert Koch... 9 Edward Jenner Growth of Medical Microbiology Staining Techniques Historical Background of Virology History of Discovery of Antibiotics Historical Background of Soil Microbiology Turning Points in Microbiological Research Microbial Biotechnology Microbial Enzyme Technology Microbial Genetic Engineering Origin, Evolution and Biodiversity in Microorganisms abiogenesis and origin of life Origins of earth and life The Appearance of Life The Original Origin-of-Life Experiment Current models of the origin of life Origin of organic molecules: Miller and Wächtershäuser's theories polymerization From organic molecules to protocells Genes first model: the RNA world (RNA world hypothesis) Inteins in Evolution Metabolism first model: Iron-sulfur world and others The Bubble Theory... 29

7 Hybrid models Other models Clay theory of the origin of life Deep-hot biosphere: Model of Gold Primitive extra-terrestrial life Which Came First - The Animal or the Plant Cell? Precursor of Life Chemical Evidences Geological Evidences Microorganisms and the Evolution of the Earth Deposition of Iron Deposition of Calcium Carbonate The Evolution of the Protists Genome Tree and the Nature of Genome Evolution Pathogenicity islands and the evolution of microbes Drug Resistance in Bacteria and Evolution Nature and Origin of Viruses Origin of Virus Genome Evolution Information, Cybernetics, and Evolution Lateral gene transfer and the origins of Procaryotic groups Microbial Biodiversity: The Natural Biological Capital of the Earth Biodiversity at Different Levels Ecosystem Diversity Microbial Biodiversity and Environment Variations Found in Bacteria Archaeal Diversity Biodiversity of Eucaryotic Microorganisms (Fungi, Algae and Protozoa) Evolution, Adaptability and Biodiversity Bacterial Progenitor Microorganisms from Cell Organelle Mitochondria are the Descended form of Bacteria? Evolution of mitochondria in protozoa The Endosymbiotic Hypothesis Cytoplasmic Membrane and Adaptability and Diversity Radiation Resistant Bacteria Procaryotes: General Account Biological Identity of Procaryotes Identification of Procaryotes ARCHAEA How Archaea differ from Bacteria Methanogens Extreme halophiles The extreme thermophiles...50

8 Bacteria Cyanobacteria Spirochetes Spirilla The Myxobacteria Lithotrophs Pseudomonads and their relatives Enterics Vibrios Nitrogen-fixing organisms Pyogenic Cocci Lactic acid bacteria Actinomycetes and related bacteria Rickettsias and chlamydiae Mycoplasmas Biological Identity of Procaryotes PROCARYOTIC STRUCTURE AND FUNCTION Procaryotic Reproduction and Genetics Ecology of Procaryotes Important books on Prokaryotes Taxonomy of Microorganisms Lower Protists (ProCaryota) Taxonomy and Classification of Procaryotes Genome trees and the nature of genome evolution What is Taxonomy? Systematics Taxonomic Ranks Binomial System Major Characteristics Used in Taxonomy Morphological Characteristics Physiological and Metabolic Characteristics Genetic analysis Molecular Characteristics Comparison of Proteins Antibody-antigen reactions in vitro Nucleic Acid Base Composition Nucleic Acid Hybridization Nucleic Acid Sequencing Classification SystemS Natural Classification Phyletic Classification Numerical Taxonomy Applications of Molecular Biology to Taxonomy DNA Hybridization... 80

9 DNA-Ribosomal RNA Hybridization Ribosomal RNA in Microbial Taxonomy Methods Used to Study the Molecular Architecture of the Procaryotic Cell Phenetic Classification and Bergey's Manual A New Kingdom of Organisms? The Kingdoms of Organisms Demerits of The Five-kingdom System The Six-kingdom System Cavalier-Smith's Eight-kingdom System Prochloron Monstrous Microbe (Epulopiscium fishelsoni) Nature, Classification, Morphology and Synthesis of Viruses Introduction GENERAL FEATURES OF VIRUSES Physical Properties of Viruses Thermal death point Longivity in vitro Dilution inactivation Host range Serological reaction Cross protection Mutation Principals of Virus Taxonomy Classification of Viruses Other criteria The current taxonomic system Virus families and hosts Diagnosis and taxonomy Presence of Viruses in Eukaryotic Microorganisms Algae Fungi Protozoa Structure and Composition of Viruses Morphology of Viruses The Structure of Viruses General Structural Properties Virion Size Detail Morphological Structures of Virus Complex Symmetry Bacteriophages of the T Even Series (T2, T4, T6) Vaccinia Virus Structural Abnormalities in Viruses Size of Viruses Surface of Virus

10 Nomenclature of Various Parts of Virus Chemical Structure and Composition of Viruses Nucleic Acids of Viruses Biology of Single Strandedness Evidences for Single Strandedness Single-stranded RNA phages Structure of Nucleic Acids Eucaryotic mrna Structure and Function Degradation of the X DNA Replication of Viral Nucleic Acid Viruses with Capsids of Complex Symmetry Parts of Viruses The Envelope Biochemical Constituents of Envelope Saellite Viruses (Viruses Requiring Helper Viruses) The Cultivation of Viruses Virus Purification and Assays Denaturation of Viruses Methodology Virus Assays Bacteriophages Classification of Bacteriophages T - Phage Phage Nucleic Acids Multiplication Cycle of Virus One Step Growth Cycle: General Aspects Eclipse Period Synthetic Phase of the Virus Multiplication Cycle Beneficial Activities of Viruses Medical use of Virulent Phages Viruses of Eucaryotes Plant Viruses Virion Morphology Classification of Plant Viruses Tobamovirus Group Tombusvirus Group Plant Virus Reproduction Transmission of Plant Viruses Virus of Fungi and Algae Plant Viruses as Gene Vectors Advantages and Disadvantages of Plant Viruses as Gene Vectors Attributes of a Putative Viral Vector Animal Viruses

11 Microbiology Fundamentals and Applications Publisher : Agrobios Publications ISBN : Author : Purohit SS Type the URL : Get this ebook