Microbiology for dummies

385 Pages·2015·12.792 MB·English

by  Jennifer Stearns, Michael Surette

Microbiology

by Jennifer C. Stearns, PhD, Julie Kaiser, MSc,
and Michael G. Surette, PhD
Microbiology For Dummies®
Published by: John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030-5774, www.wiley.com
Copyright © 2015 by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
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Library of Congress Control Number: 2014936394
ISBN 978-1-118-87118-8 (pbk); ISBN 978-1-118-87126-3 (ebk); ISBN 978-1-118-87131-7 (ebk)
Manufactured in the United States of America
10 9 8 7 6 5 4 3 2 1
Contents at a Glance
Introduction ................................................................ 1
Part I: Getting Started with Microbiology ...................... 5
Chapter 1: Microbiology and You ....................................................................................7
Chapter 2: Microbiology: The Young Science ..............................................................11
Chapter 3: Microbes: They’re Everywhere and They Can Do Everything ................21
Part II: Balancing the Dynamics of Microbial Life ........ 29
Chapter 4: Understanding Cell Structure and Function ..............................................31
Chapter 5: Making Sense of Metabolism .......................................................................49
Chapter 6: Get ting the Gist of Microbial Genetics .......................................................67
Chapter 7: Measuring Microbial Growth ......................................................................89
Part III: Sorting Out Microbial Diversity .................... 105
Chapter 8: Appreciating Microbial Ancestry ..............................................................107
Chapter 9: Harnessing Energy, Fixing Carbon ............................................................121
Chapter 10: Comparing Respiration and Fermentation ............................................141
Chapter 11: Uncovering a Variety of Habitats ............................................................157
Part IV: Meeting the Microbes .................................. 179
Chapter 12: Meet the Prokaryotes ...............................................................................181
Chapter 13: Say Hello to the Eukaryotes ....................................................................199
Chapter 14: Examining the Vastness of Viruses ........................................................219
Part V: Seeing the Impact of Microbes ....................... 237
Chapter 15: Understanding Microbes in Human Health and Disease .....................239
Chapter 16: Putting Microbes to Work: Biotechnology ............................................261
Chapter 17: Fighting Microbial Diseases.....................................................................283
Part VI: New Frontiers in Microbiology ...................... 299
Chapter 18: Teasing Apart Communities ....................................................................301
Chapter 19: Synthesizing Life .......................................................................................313
Part VII: The Part of Tens ......................................... 325
Chapter 20: Ten (Or So) Diseases Caused by Microbes ...........................................327
Chapter 21: Ten Great Uses for Microbes...................................................................335
Chapter 22: Ten Great Uses for Microbiology ............................................................341
Index ...................................................................... 349
Table of Contents
Introduction ................................................................. 1
About This Book ..............................................................................................1
Foolish Assumptions .......................................................................................2
Icons Used in This Book .................................................................................2
Beyond the Book .............................................................................................3
Where to Go from Here ...................................................................................3
Part I: Getting Started with Microbiology ....................... 5
Chapter 1: Microbiology and You . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Why Microbiology? ..........................................................................................7
Introducing the Microorganisms ...................................................................8
Deconstructing Microbiology ........................................................................9
Chapter 2: Microbiology: The Young Science . . . . . . . . . . . . . . . . . . . . 11
Before Microbiology: Misconceptions and Superstitions ........................11
Discovering Microorganisms .......................................................................12
Debunking the myth of spontaneous generation.............................13
Improving medicine, from surgery to antibiotics and more ..........14
Looking at microbiology outside the human body .........................16
The Future of Microbiology ..........................................................................16
Exciting frontiers..................................................................................17
Remaining challenges ..........................................................................18
Chapter 3: Microbes: They’re Everywhere and 
They Can Do Everything . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Habitat Diversity ............................................................................................22
Metabolic Diversity .......................................................................................24
Getting energy ......................................................................................25
Capturing carbon .................................................................................25
Making enzymes ...................................................................................25
Secondary metabolism ........................................................................26
The Intersection of Microbes and Everyone Else ......................................27
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Microbiology For Dummies
Part II: Balancing the Dynamics of Microbial Life ........ 29
Chapter 4: Understanding Cell Structure and Function . . . . . . . . . . . . 31
Seeing the Shapes of Cells ............................................................................31
Life on a Minute Scale: Considering the Size of Prokaryotes ...................33
The Cell: An Overview ...................................................................................34
Scaling the Outer Membrane and Cell Walls ..............................................35
Examining the outer membrane .........................................................35
Exploring the cell wall .........................................................................37
Other Important Cell Structures ..................................................................41
Divining Cell Division ....................................................................................43
Tackling Transport Systems ........................................................................44
Coasting with the current: Passive transport ..................................45
Upstream paddle: Active transport ...................................................46
Keeping things clean with efflux pumps ...........................................46
Getting Around with Locomotion ................................................................47
Chapter 5: Making Sense of Metabolism . . . . . . . . . . . . . . . . . . . . . . . . 49
Converting with Enzymes .............................................................................49
In Charge of Energy: Oxidation and Reduction ..........................................51
Donating and accepting electrons .....................................................52
Bargaining with energy-rich compounds ..........................................54
Storing energy for later .......................................................................55
Breaking Down Catabolism ..........................................................................56
Digesting glycolysis .............................................................................56
Stepping along with respiration and electron carriers ...................57
Moving with the proton motive force ...............................................59
Turning the citric acid cycle ..............................................................60
Stacking Up with Anabolism ........................................................................61
Creating amino acids and nucleic acids ...........................................62
Making sugars and polysaccharides .................................................63
Putting together fatty acids and lipids ..............................................65
Chapter 6: Get ting the Gist of Microbial Genetics . . . . . . . . . . . . . . . . 67
Organizing Genetic Material .........................................................................67
DNA: The recipe for life .......................................................................68
Perfect plasmids ..................................................................................70
Doubling down with DNA replication ................................................71
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Table of Contents
Assembling the Cellular Machinery ............................................................75
Making messenger RNA.......................................................................75
Remembering other types of RNA .....................................................77
Synthesizing protein ............................................................................78
Making the Right Amount: Regulation ........................................................80
Turning the tap on and off: DNA regulation .....................................81
Regulating protein function ................................................................83
Changing the Genetic Code ..........................................................................83
Slight adjustments ...............................................................................84
Major rearrangements .........................................................................86
Chapter 7: Measuring Microbial Growth . . . . . . . . . . . . . . . . . . . . . . . . 89
Getting Growth Requirements Right ...........................................................89
Physical requirements ........................................................................89
Chemical requirements .......................................................................91
Culturing microbes in the lab .............................................................92
Observing Microbes ......................................................................................94
Counting small things ..........................................................................95
Seeing morphology ..............................................................................97
Calculating Cell Division and Population Growth .....................................99
Dividing cells ........................................................................................99
Following growth phases ....................................................................99
Inhibiting Microbial Growth .......................................................................101
Physical methods ...............................................................................102
Disinfectants .......................................................................................103
Part III: Sorting Out Microbial Diversity ..................... 105
Chapter 8: Appreciating Microbial Ancestry . . . . . . . . . . . . . . . . . . . . 107
Where Did Microbes Come From? .............................................................107
Tracing the origins of life ..................................................................108
Diversifying early prokaryotes .........................................................108
The impact of prokaryotes on the early earth ...............................109
Hitching a ride: Endosymbiosis .......................................................110
Understanding Evolution ............................................................................113
Studying Evolution ......................................................................................115
Choosing marker genes .....................................................................115
Seeing the direction of gene transfer in prokaryotes ....................116
Classifying and Naming Microbes .............................................................117
Climbing the Tree of Life ............................................................................119
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Microbiology For Dummies
Chapter 9: Harnessing Energy, Fixing Carbon . . . . . . . . . . . . . . . . . . . 121
Forging Ahead with Autotrophic Processes ............................................121
Fixing carbon ......................................................................................122
Using the Energy in Light ............................................................................125
Harvesting light: Chlorophylls and bacteriochlorophylls ............126
Helping photosynthesis out: Carotenoids and phycobilins .........129
Generating oxygen (or not): Oxygenic and 
anoxygenic photosynthesis ..........................................................130
Getting Energy from the Elements: Chemolithotrophy ..........................135
Harnessing hydrogen ........................................................................136
Securing electrons from sulfur .........................................................136
Pumping iron ......................................................................................137
Oxidizing nitrate and ammonia ........................................................138
Chapter 10: Comparing Respiration and Fermentation . . . . . . . . . . . . 141
Lifestyles of the Rich and Facultative .......................................................141
Seeing the Big Picture .................................................................................143
Digging into Respiration .............................................................................146
Spinning the citric acid cycle ...........................................................146
Stepping down the electron transport chain .................................148
Respiring anaerobically ....................................................................150
Figuring Out Fermentation .........................................................................153
Chapter 11: Uncovering a Variety of Habitats . . . . . . . . . . . . . . . . . . . 157
Defining a Habitat ........................................................................................158
Understanding Nutrient Cycles .................................................................159
Carbon cycling ...................................................................................159
Nitrogen cycling .................................................................................162
Sulfur cycling ......................................................................................164
Phosphorous cycles in the ocean ....................................................164
Microbes Socializing in Communities .......................................................165
Using quorum sensing to communicate .........................................165
Living in biofilms ................................................................................166
Exploring microbial mats ..................................................................167
Discovering Microbes in Aquatic and Terrestrial Habitats ...................168
Thriving in water ................................................................................168
Swarming soils ...................................................................................170
Getting Along with Plants and Animals ....................................................170
Living with plants...............................................................................172
Living with animals ............................................................................174
Living with insects .............................................................................174
Living with ocean creatures .............................................................175
Tolerating Extreme Locations ....................................................................175
Detecting Microbes in Unexpected Places ...............................................176