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Microbiology For Dummies (9781119544425) was previously published as Microbiology For Dummies (9781118871188). While this version features a new Dummies cover and design, the content is the same as the prior release and should not be considered a new or updated product.
Microbiology is the study of life itself, down to the smallest particle
Microbiology is a fascinating field that explores life down to the tiniest level. Did you know that your body contains more bacteria cells than human cells? It's true. Microbes are essential to our everyday lives, from the food we eat to the very internal systems that keep us alive. These microbes include bacteria, algae, fungi, viruses, and nematodes. Without microbes, life on Earth would not survive. It's amazing to think that all life is so dependent on these microscopic creatures, but their impact on our future is even more astonishing. Microbes are the tools that allow us to engineer hardier crops, create better medicines, and fuel our technology in sustainable ways. Microbes may just help us save the world.
Microbiology For Dummies is your guide to understanding the fundamentals of this enormously-encompassing field. Whether your career plans include microbiology or another science or health specialty, you need to understand life at the cellular level before you can understand anything on the macro scale.
You need to know how cells work, how they get nutrients, and how they die. You need to know the effects different microbes have on different systems, and how certain microbes are integral to ecosystem health. Microbes are literally the foundation of all life, and they are everywhere. Microbiology For Dummies will help you understand them, appreciate them, and use them.
Jennifer C. Stearns, PhD, is an Assistant Professor in the Department of Medicine at McMaster University. She studies how we get our gut microbiome in early life and how it can keep us healthy over time. Michael G. Surette, PhD, is a Professor in the Department of Medicine at McMaster University, where he pushes the boundaries of microbial research. Julienne C. Kaiser, PhD, is a doctoral career educator.
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
Chapter 2
IN THIS CHAPTER
Remembering a time before microbiology
Discovering microorganisms step-by-step
Looking forward
Compared with other more ancient fields of science, microbiology is a relative baby. Physics began in ancient times, mathematics even earlier, but the knowledge of tiny living things, their biology, and their impact on human lives has only been around since the late 19th century. Until about the 1880s, people still believed that life could form out of thin air and that sickness was caused by sins or bad odors.
As with other fields in science, there are two aspects to microbiology research: basic and applied. Basic microbiology is about discovering the fundamental rules governing the microbial world and studying all the variety of microbial life and microbial systems. Applied microbiology is more about solving a problem and involves using microbes and their genes or proteins for practical purposes such as in industry and medicine.
In this chapter, we introduce the key concepts and experiments that gave rise to the discovery of microbes and their importance in disease. This chapter also highlights the many different areas of study within microbiology and some advances and challenges in the prevention and treatment of infectious diseases.
Medical practices in ancient times were all heavily tinged with supernatural beliefs. Ancient Egypt was ahead of its time in terms of medicine, with physicians performing surgery and treating a wide variety of conditions. Medicine in India was also quite advanced. Ancient Greek physicians were concerned with balancing the body's humors (the four distinct body fluids that they believed were responsible for health when in balance, or disease when out of balance), and medicine in medieval Europe was based on this tradition. None, however, had knowledge of the microbial causes of disease.
Opinions about why diseases afflicted people differed between cultures and parts of society, and the treatments differed as well. Diseases were thought to be caused by
Although the concept of contagion was known, it wasn't attributed to tiny living creatures but to bad odors or spirits, such as the devil. So, simple measures, such as removing sources of infection or washing hands or surgical equipment, were simply not done.
Before microorganisms were discovered, life was not known to arise uniquely from living cells; instead, it was thought to spring spontaneously from mud and lakes or anywhere with sufficient nutrients in a process called spontaneous generation. This concept was so compelling that it persisted until late into the 19th century.
Robert Hooke, a 17th-century English scientist, was the first to use a lens to observe the smallest unit of tissues he called "cells." Soon after, the Dutch amateur biologist Anton van Leeuwenhoek observed what he called "animacules" with the use of his homemade microscopes.
When microorganisms were known to exist, most scientists believed that such simple life forms could surely arise through spontaneous generation. So, when they heated a container, placed a nutrient broth (a mixture of nutrients that supported growth of microorganisms in these early experiments) in the container and then sealed it, and no microorganisms appeared, they believed it had to be due to the absence of either air or the vital force (whatever that was!) necessary to make life.
The concept of spontaneous generation was finally put to rest by the French chemist Louis Pasteur in an inspired set of experiments involving a goose-necked flask (see Figure 2-1). When he boiled broth in a flask with a straight neck and left it exposed to air, organisms grew. When he did this with his goose-necked flask, nothing grew. The S-shape of this second flask trapped dust particles from the air, preventing them from reaching the broth. By showing that he could allow air to get into the flask but not the particles in the air, Pasteur proved that it was the organisms in the dust that were growing in the broth. This is the principle behind the Petri dish used to grow bacteria on solid growth medium (made by adding a gelling material to the broth), which allows air but not small particles to reach the surface of the growth medium.
FIGURE 2-1: Pasteur's experiments that disproved the theory of spontaneous generation.
The idea that invisible microorganisms are the cause of disease is called germ theory. This was another of the important contributions of Pasteur to microbiology. It emerged not only from his experiments disproving spontaneous generation but also from his search for the infectious organism (typhoid) that caused the deaths of three of his daughters.
Around the same time that Pasteur was doing his experiments, a doctor named Robert Koch was working on finding the causes of some very nasty animal diseases (first anthrax, and then tuberculosis). He devised a strict set of guidelines - named Koch's postulates - that are still used to this day to definitively prove that a microorganism causes a particular disease. Koch's four postulates are
Once scientists knew that microbes caused disease, it was only a matter of time before medical practices improved dramatically. Surgery used to be as dangerous as not doing anything at all, but once aseptic (sterile) technique was introduced, recovery rates improved dramatically. Hand washing and quarantine of infected patients reduced the spread of disease and made hospitals into a place to get treatment instead of a place to die.
Vaccination was discovered before germ theory, but it wasn't fully understood until the time of Pasteur. In the late 18th century, milkmaids who contracted the nonlethal cowpox sickness from the cows they were milking were spared in deadly smallpox outbreaks that ravaged England periodically. The physician Edward Jenner used pus from cowpox scabs to vaccinate people against smallpox. Years later, Pasteur realized that the reason this worked was that the cowpox virus was similar enough to the smallpox virus to kickstart an immune response that would provide a person with long-term protection, or immunity.
Antibiotics were discovered completely by accident in the 1920s, when a solid culture in a Petri dish (called a plate) of bacteria was left to sit around longer than usual. As will happen with any food source left sitting around, it became moldy, growing a patch of fuzzy fungus. The colonies in the area around the fungal colony were smaller in size and seemed to be growing poorly compared to the bacteria on the rest of the plate, as shown in Figure 2-2.
FIGURE 2-2: Antibacterial property of the fungus Penicillium.
The compound found to be responsible for this antibacterial action was named penicillin. The first antibiotic, penicillin was later used to treat people suffering from a variety of bacterial infections and to prevent bacterial infection in burn victims, among many other applications.
After bacteria were discovered, the field of molecular biology made great strides in understanding the genetic code, how DNA is regulated, and how RNA is translated into proteins. Until this point, research was focused mainly on plant and animal cells, which are much more complex than bacterial cells. When researchers switched to studying these processes in bacteria, many of the secrets of genes and enzymes started to reveal themselves.
Microorganisms are named using the Linnaeus system developed in the 18th century. It uses two-part Latin names for all living things. The first part, which is capitalized, is a genus name given to closely related organisms; the second part is a species name, which is not capitalized, given to define a specific organism. This is more challenging than you may think, even for plants and animals, and the concept of a species of microorganism is a slippery one (see Chapter 8 for more information). When the complete genus and species name for an organism has been introduced, it can be referred to by only the first letter of the genus with the complete species name after it (for example, Escherichia coli is abbreviated as E. coli), but both are always italicized.
Two important microbiologists helped shape our understanding of the microbial world outside the human body and gave rise to modern-day environmental microbiology:
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