Essential Microbiology
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JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 Essential Microbiology i JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 ii JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 Essential Microbiology Stuart Hogg The University of Glamorgan, UK iii JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 Copyright C 2005 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England Telephone (+44) 1243 779777 Email (for orders and customer service enquiries): [email protected] Visit our Home Page on www.wileyeurope.com or www.wiley.com Reprinted with corrections September 2005 All Rights Reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except under the terms of the Copyright, Designs and Patents Act 1988 or under the terms of a licence issued by the Copyright Licensing Agency Ltd, 90 Tottenham Court Road, London W1T 4LP, UK, without the permission in writing of the Publisher. Requests to the Publisher should be addressed to the Permissions Department, John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England, or emailed to [email protected], or faxed to (+44) 1243 770620. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The Publisher is not associated with any product or vendor mentioned in this book. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold on the understanding that the Publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Other Wiley Editorial Offices John Wiley & Sons Inc., 111 River Street, Hoboken, NJ 07030, USA Jossey-Bass, 989 Market Street, San Francisco, CA 94103-1741, USA Wiley-VCH Verlag GmbH, Boschstr. 12, D-69469 Weinheim, Germany John Wiley & Sons Australia Ltd, 33 Park Road, Milton, Queensland 4064, Australia John Wiley & Sons (Asia) Pte Ltd, 2 Clementi Loop #02-01, Jin Xing Distripark, Singapore 129809 John Wiley & Sons Canada Ltd, 22 Worcester Road, Etobicoke, Ontario, Canada M9W 1L1 Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Library of Congress Cataloguing-in-Publication Data British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN 0 471 49753 3 (hbk) 0 471 49754 1 (pbk) Typeset in 10/12pt Sabon by TechBooks, New Delhi, India Printed and bound in Great Britain by Antony Rowe, Ltd, Chippenham, Wiltshire This book is printed on acid-free paper responsibly manufactured from sustainable forestry in which at least two trees are planted for each one used for paper production. iv JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 Contents Preface ix Acknowledgements xi Part I Introduction 1 1 Microbiology: What, Why and How? 3 What is microbiology? 3 Why is microbiology important? 3 How do we know? Microbiology in perspective: to the ‘golden age’ and beyond 4 Light microscopy 10 Electron microscopy 15 2 Biochemical Principles 17 Atomic structure 17 Acids, bases, and pH 25 Biomacromolecules 27 Test yourself 48 3 Cell Structure and Organisation 51 The procaryotic cell 54 The eucaryotic cell 65 Cell division in procaryotes and eucaryotes 72 Test yourself 75 Part II Microbial Nutrition, Growth and Metabolism 77 4 Microbial Nutrition and Cultivation 79 Nutritional categories 81 How do nutrients get into the microbial cell? 83 Laboratory cultivation of microorganisms 84 Test yourself 89 5 Microbial Growth 91 Estimation of microbial numbers 91 Factors affecting microbial growth 96 The kinetics of microbial growth 101 v JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 vi CONTENTS Growth in multicellular microorganisms 105 Test yourself 106 6 Microbial Metabolism 109 Why is energy needed? 109 Enzymes 110 Principles of energy generation 118 Anabolic reactions 148 The regulation of metabolism 154 Test yourself 155 Part III Microbial Diversity 157 A few words about classification 158 7 Procaryote Diversity 163 Domain: Archaea 164 Domain: Bacteria 169 Bacteria and human disease 192 Test yourself 195 8 The Fungi 197 General biology of the Fungi 198 Classification of the Fungi 199 Fungi and disease 208 Test yourself 209 9 The Protista 211 ‘The Algae’ 211 ‘The Protozoa’ 224 The slime moulds and water moulds (the fungus-like protists) 230 Protistan taxonomy: a modern view 234 Test yourself 234 10 Viruses 237 What are viruses? 237 Viral structure 238 Classification of viruses 243 Viral replication cycles 244 Viroids 255 Prions 256 Cultivating viruses 256 Viral diseases in humans 259 Test yourself 264 Part IV Microbial Genetics 267 11 Microbial Genetics 269 How do we know genes are made of DNA? 269 DNA replication 271 JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 CONTENTS vii What exactly do genes do? 275 Regulation of gene expression 285 The molecular basis of mutations 288 Genetic transfer in microorganisms 299 Test yourself 312 12 Microorganisms in Genetic Engineering 315 Introduction 315 Plasmid cloning vectors 319 Bacteriophages as cloning vectors 323 Expression vectors 326 Eucaryotic cloning vectors 328 Polymerase chain reaction (PCR) 333 Test yourself 335 Part V Control of Microorganisms 337 13 The Control of Microorganisms 339 Sterilisation 339 Disinfection 344 The kinetics of cell death 347 Test yourself 351 14 Antimicrobial Agents 353 Antibiotics 355 Resistance to antibiotics 364 Antibiotic susceptibility testing 367 Antifungal and antiviral agents 368 The future 371 Test yourself 372 Part VI Microorganisms in the Environment 375 15 Microbial Associations 377 Microbial associations with animals 377 Microbial associations with plants 379 Microbial associations with other microorganisms 383 Test yourself 386 16 Microorganisms in the Environment 389 The carbon cycle 390 The nitrogen cycle 390 The sulphur cycle 393 Phosphorus 394 The microbiology of soil 394 The microbiology of freshwater 396 The microbiology of seawater 397 Detection and isolation of microorganisms in the environment 398 Beneficial effects of microorganisms in the environment 399 JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 viii CONTENTS Harmful effects of microorganisms in the environment 402 Test yourself 403 Part VII Microorganisms in Industry 405 17 Industrial and Food Microbiology 407 Microorganisms and food 407 Microorganisms as food 413 The microbial spoilage of food 414 Microorganisms in the production of biochemicals 414 Products derived from genetically engineered microorganisms 418 Microorganisms in wastewater treatment and bioremediation 420 Microorganisms in the mining industry 420 Test yourself 422 Glossary 425 Appendix 447 Further Reading 449 Index 454 JWBK011-FM JWBK011-Hogg August 12, 2005 19:44 Char Count= 0 Preface Every year, in UK universities alone, many hundreds of students study microbiology as part of an undergraduate course. For some, the subject will form the major part of their studies, leading to a BSc degree in Microbiology, or a related subject such as Bacteriology or Biotechnology. For the majority, however, the study of microbiology will be a brief encounter, forming only a minor part of their course content. A number of excellent and well-established textbooks are available to support the study of microbiology; such titles are mostly over 1000 pages in length, beautifully illustrated in colour, and rather expensive. This book in no way seeks to replace or compete with such texts, which will serve specialist students well throughout their three years of study, and represent a sound investment. It is directed rather towards the second group of students, who require a text that is less detailed, less comprehensive, and less expensive! The majority of the students in my own classes are enrolled on BSc degrees in Biology, Human Biology and Forensic Science; I have felt increasingly uncomfortable about recommending that they invest a substantial sum of money on a book much of whose content is irrelevant to their needs. Alternative recommendations, however, are not thick on the ground. This, then, was my initial stimulus to write a book of ‘microbiology for the non-microbiologist’. The facts and principles you will find here are no different from those described elsewhere, but I have tried to select those topics that one might expect to encounter in years 1 and 2 of a typical non-specialist degree in the life sciences or related disciplines. Above all, I have tried to explain concepts or mechanisms; one thing my research for this book has taught me is that textbooks are not always right, and they certainly don’t always explain things as clearly as they might. It is my wish that the present text will give the attentive reader a clear understanding of sometimes complex issues, whilst avoiding over-simplification. The book is arranged into seven sections, the fourth of which, Microbial Genetics, acts as a pivot, leading from principles to applications of microbiology. Depending on their starting knowledge, readers may ‘dip into’ the book at specific topics, but those whose biological and chemical knowledge is limited are strongly recommended to read Chapters 2 and 3 for the foundation necessary for the understanding of later chapters. Occasional boxes are inserted into the text, which provide some further enlightenment on the topic being discussed, or offer supplementary information for the inquisitive reader. As far as possible, diagrams are limited to simple line drawings, most of which could be memorised for reproduction in an examination setting.