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 1: Getting Started With Microbiology 5
Chapter 1: Microbiology and You 7
Why Microbiology? 7
Introducing the Microorganisms 8
Deconstructing Microbiology 10
Chapter 2: Microbiology: The Young Science 11
Before Microbiology: Misconceptions and Superstitions 12
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 23
Metabolic Diversity 24
Getting energy 25
Capturing carbon 25
Making enzymes 26
Secondary metabolism 26
The Intersection of Microbes and Everyone Else 27
Part 2: 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: Getting the Gist of Microbial Genetics 67
Organizing Genetic Material 68
DNA: The recipe for life 68
Perfect plasmids 70
Doubling down with DNA replication 71
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 83
Major rearrangements 85
Chapter 7: Measuring Microbial Growth 89
Getting Growth Requirements Right 89
Physical requirements 90
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 98
Dividing cells 99
Following growth phases 100
Inhibiting Microbial Growth 101
Physical methods 101
Disinfectants 102
Part 3: Sorting Out Microbial Diversity 103
Chapter 8: Appreciating Microbial Ancestry 105
Where Did Microbes Come From? 105
Tracing the origins of life 106
Diversifying early prokaryotes 107
The impact of prokaryotes on the early earth 107
Hitching a ride: Endosymbiosis 108
Understanding Evolution 111
Studying Evolution 113
Choosing marker genes 113
Seeing the direction of gene transfer in prokaryotes 114
Classifying and Naming Microbes 115
Climbing the Tree of Life 117
Chapter 9: Harnessing Energy, Fixing Carbon 119
Forging Ahead with Autotrophic Processes 120
Fixing carbon 120
Using the Energy in Light 124
Harvesting light: Chlorophylls and bacteriochlorophylls 125
Helping photosynthesis out: Carotenoids and phycobilins 127
Generating oxygen (or not): Oxygenic and anoxygenic photosynthesis 128
Getting Energy from the Elements: Chemolithotrophy 133
Harnessing hydrogen 134
Securing electrons from sulfur 134
Pumping iron 135
Oxidizing nitrate and ammonia 136
Chapter 10: Comparing Respiration and Fermentation 139
Lifestyles of the Rich and Facultative 139
Seeing the Big Picture 141
Digging into Respiration 144
Spinning the citric acid cycle 144
Stepping down the electron transport chain 146
Respiring anaerobically 147
Figuring Out Fermentation 150
Chapter 11: Uncovering a Variety of Habitats 155
Defining a Habitat 156
Understanding Nutrient Cycles 157
Carbon cycling 157
Nitrogen cycling 160
Sulfur cycling 162
Phosphorous cycles in the ocean 162
Microbes Socializing in Communities 163
Using quorum sensing to communicate 163
Living in biofilms 163
Exploring microbial mats 165
Discovering Microbes in Aquatic and Terrestrial Habitats 165
Thriving in water 166
Swarming soils 167
Getting Along with Plants and Animals 168
Living with plants 169
Living with animals 171
Living with insects 172
Living with ocean creatures 172
Tolerating Extreme Locations 173
Detecting Microbes in Unexpected Places 174
Part 4: Meeting the Microbes 175
Chapter 12: Meet the Prokaryotes 177
Getting to Know the Bacteria 178
The Gram-negative bacteria: Proteobacteria 178
More Gram-negative bacteria 182
The Gram-positive bacteria 186
Acquainting Yourself with the Archaea 188
Some like it scalding: Extreme thermophiles 190
Going beyond acidic: Extreme acidophiles 191
Super salty: Extreme halophiles 192
Not terribly extreme Archaea 193
Chapter 13: Say Hello to the Eukaryotes 195
Fun with Fungi 196
Figuring out fungal physiology 196
Itemizing fungal diversity 199
Interacting with plant roots 201
Ask us about the Ascomycetes 202
Mushrooms: Basidiomycetes 203
Perusing the Protists 204
Making us sick: Apicoplexans 205
Making plants sick: Oomycetes 207
Chasing amoeba and ciliates 207
Encountering the algae 210
Chapter 14: Examining the Vastness of Viruses 215
Hijacking Cells 215
Frugal viral structure 216
Simplifying viral function 217
Making Heads or Tails of Bacteriophage 219
Lytic phage 219
Temperate phage 220
Transposable phage 222
Discussing Viruses of Eukaryotes 224
Infecting animal cells 224
Following plant viruses 227
How Host Cells Fight Back 229
Restriction enzymes 229
CRISPR 230
Interfering with RNA viruses: RNAi 232
Part 5: Seeing the Impact Of Microbes 233
Chapter 15: Understanding Microbes in Human Health and Disease 235
Clarifying the Host Immune Response 236
Putting up barriers to infection 236
Raising a red flag with inflammation 237
Holding down the fort with innate immunity 237
Sending out the troops for adaptive immunity 238
Antibodies in action 240
Relying on Antimicrobials for Treating Disease 243
Fundamental features of antibiotics 244
Targets of destruction 245
Unraveling microbial drug resistance 247
Discovering new antibiotics 249
Searching Out Superbugs 250
Staying ahead of vancomycin-resistant enterococci 251
Battling methicillin-resistant Staphylococcus aureus 251
Outcompeting Clostridium difficile 253
Pressure from extended-spectrum beta-lactamases 253
Knowing the Benefits of Prebiotics and Probiotics 254
Attacking Viruses with Antiviral Drugs 255
Chapter 16: Putting Microbes to Work: Biotechnology 257
Using Recombinant DNA Technology 258
Making the insert 258
Employing plasmids 261
Cutting with restriction enzymes 262
Getting microbes to take up DNA 264
Using promoters to drive expression 267
Making use of expression vectors 267
Properly folding proteins 268
Being mindful of metabolic load 269
Making long, multi-gene constructs 269
Providing Therapies 272
Improving antibiotics 272
Developing vaccines 272
Using Microbes Industrially 273
Protecting plants with microbial insecticides 274
Making biofuels 275
Bioleaching metals 276
Cleaning up with microbes 276
Chapter 17: Fighting Microbial Diseases 279
Protecting Public Health: Epidemiology 279
Tracking diseases 280
Investigating outbreaks 280
Identifying a Microbial Pathogen 283
Characterizing morphology 283
Using biochemical tests 284
Typing strains with phage 286
Using serology 287
Testing antibiotic susceptibility 288
Understanding Vaccines 289
Understanding how vaccines work 290
Ranking the types of vaccines 291
Part 6: New Frontiers in Microbiology 293
Chapter 18: Teasing Apart Communities 295
Studying Microbial Communities 295
Borrowing from ecology 296
Seeing what sets microbial communities apart from plants and animals 296
Observing Communities: Microbial Ecology Methods 297
Selecting something special with enrichment 297
Seeing cells through lenses 298
Measuring microbial activity 299
Identifying species using marker genes 300
Getting the Hang of Microbial Genetics and Systematics 301
Sequencing whole genomes 301
Using metagenomics to study microbial communities 302
Reading microbial transcriptomics 303
Figuring out proteomics and metabolomics 304
Looking for Microbial Dark Matter 306
Chapter 19: Synthesizing Life 307
Regulating Genes: The lac Operon 308
Using a good natural system 308
Improving a good system 310
Designing Genetic Networks 312
Switching from one state to another 313
Oscillating between states 314
Keeping signals short 315
The Synthetic Biologist’s Toolbox 315
Making it modular 315
Participating in the iGEM competition 316
Part 7: The Part of Tens 319
Chapter 20: Ten (or So) Diseases Caused by Microbes 321
Ebola 322
Anthrax 322
Influenza 323
Tuberculosis 324
HIV 324
Cholera 325
Smallpox 325
Primary Amoebic Menigoencephalitis 326
The Unknown 327
Chapter 21: Ten Great Uses for Microbes 329
Making Delicious Foods 329
Growing Legumes 330
Brewing Beer, Liquor, and Wine 330
Killing Insect Pests 331
Treating Sewage 331
Contributing to Medicine 332
Setting Up Your Aquarium 332
Making and Breaking Down Biodegradable Plastics 333
Turning Over Compostable Waste 333
Maintaining a Balance 334
Chapter 22: Ten Great Uses for Microbiology 335
Medical Care: Keeping People Healthy 335
Dental Care: Keeping Those Pearly Whites Shining Bright 336
Veterinary Care: Helping Fido and Fluffy to Feel Their Best 337
Monitoring the Environment 338
Making Plants Happy 339
Keeping Fish Swimming Strong 339
Producing Food, Wine, and Beer 340
Science Hacking 341
Looking for Microbes in Clean Rooms 341
Producing Pharmaceuticals 342
Index 343
