PART I Foundations of Microbiology

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© Jones & Bartlett Learning, LLC © Jones & Bartlett OR DISTRIBUTION NOT FOR SALE © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION rin Information Flow and Genetics Metabolic Pathways Cell Structure and Cell Structure Function P Evolution Impact of Microorganisms Microbial Systems Microbial Chapter 6 concepts as described in aspects of the six principal (overarching) several The six chapters in Part I embrace curriculum. concept-based microbiology Statements for a the ASM Fundamental

of Microbiology Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Foundations Foundations I PART

9781284101041_CH01_001_034.indd 1

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NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC

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CHAPTER 1 Chapter preVieW © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION 1.1 TheNOT Discovery FOR SALE of Microbes OR DISTRIBUTION Leads to Questioning Their Origins Microbiology: Microbiology Pathways: Being a Scientist © Jones & Bartlett Learning, LLC © Jones & BartlettInvestigating Learning, the Microbial LLC World 1: NOT FORThen SALE OR DISTRIBUTION and Now NOT FOR SALECan Life OR Arise DISTRIBUTION Spontaneously? MicroInquiry 1: Scientifi c Inquiry and Spontaneous Generation Space. The fi nal frontier! Really? The fi nal frontier? The image on the right in the chapter opening illus- 1.2 Disease Transmission Can Be Prevented tration shows one of© an Jones estimated & Bartlett 350 billion Learning, large LLC Clinical Case 1: Childbed Fever : A © Jones & Bartlett Learning, LLC 24 galaxies and more thanNOT 10 FOR stars SALE in the ORvisible DISTRIBUTION uni- Historical Refl ection NOT FOR SALE OR DISTRIBUTION verse. However, the invisible microbial universe on The Classical Golden Age of Earth consists of more than 10 30 microorganisms (or 1.3 Microbiology Reveals the Germ microbes for short) distributed among an estimated 1 trillion (10 12) species. As the image on the left 1.4 With the Discovery of Other Microbes, shows,© Jonesmicrobes & mightBartlett be microscopicLearning, LLCin size, but the© Jones Microbial & WorldBartlett Expands Learning, LLC they NOTare magnifi FOR centSALE in theirOR DISTRIBUTIONevolutionary diversity 1.5 ANOT Second FOR Golden SALE Age OR of Microbiology DISTRIBUTION and astounding in their sheer numbers. Together, Involves the Birth of Molecular Biology we can refer to the global community of microbes and Chemotherapy and their genes as Earth’s microbiome . 1.6 A Third Golden Age of Microbiology Is Now © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC A Day in the Life of a Microorganism NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Because microorganisms exist in such diversity and vast numbers in the oceans, landmasses, and atmo- The Oceans sphere, they must play important roles in the very The oceans and seas cover more than 70% of planet survival of other organisms on the planet. Conse- Earth and represent the foundation that maintains quently, could understanding© Jones & these Bartlett microscopic Learning, LLCour planet in a habitable© condition. Jones & A Bartlett critical fac-Learning, LLC organisms on EarthNOT be as FOR important SALE asOR studying DISTRIBUTION tor in this maintenance isNOT the marineFOR SALE microbiome, OR DISTRIBUTION stars and galaxies in space? Let’s uncover but a few which, composed of some 3 × 10 29 microbes, dom- examples of what a “day in the life of a microorgan- inates ocean life. High densities of these organism” is like in shaping the fundamental life pro- isms can be found anywhere from the frozen polar cesses around the globe. regions to the hot, volcanic thermal vents and the © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Photographic image of nearby galaxies in space (right) and a light microscope image (left) of bacterial cells (larger dots), © Jones &viruses Bartlett (smaller Learning, dots), and a LLCdiatom (center). © Jones & Bartlett Learning, LLC NOT FOR (left) SALE Courtesy of JedOR Alan Fuhrman,DISTRIBUTION University of Southern California. (right) Courtesy of JPL-Caltech/NASA.NOT FOR SALE OR DISTRIBUTION

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© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORcold SALE seeps OR on DISTRIBUTIONthe dark seafl oor. Making up 90% ofNOT soilFOR can SALE have up OR to DISTRIBUTION1013 microbes living in the water- the ocean biomass, this marine microbiome is criti- fi lled pore spaces in the soil (FIGURE 1.1 B ). cal to regulating life on Earth. This diverse soil microbiome is responsible for Every day, many of the dwellers in this microbial many daily activities essential to life. Here are some community perform the following: of the activities soil microorganisms perform: © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC ▶ Create the foundation for all marine food ▶ Carry out 90% of all biochemical reactions webs by performingNOT FOR photosynthesisSALE OR DISTRIBUTION (in occurring in the soil.NOT FOR SALE OR DISTRIBUTION sunlit areas) and chemosynthesis (in dark ▶ Recycle dead plant and animal material and areas) to convert carbon into sugars and return carbon dioxide to the atmosphere. nutrients on which all fi sh and ocean mam- ▶ Represent a source for many of today’s anti- © Jonesmals directly & Bartlett or indirectly Learning, depend. LLC biotics.© Jones & Bartlett Learning, LLC ▶NOT Provide FOR upSALE to 50% OR ofDISTRIBUTION the oxygen gas we ▶ ProvideNOT FORplants SALE with ORimportant DISTRIBUTION nutrients, breathe and many other organisms use to such as nitrogen, sulfur, and phosphorus. stay alive by performing photosynthesis Think of it this way—microbes are helping (FIGURE 1.1 A ). to feed the world. ▶ Control atmospheric aerosols and cloud for- Microbes also can degrade pesticides and other © Jones & Bartlettmation Learning, through LLCthe sea spray ejected into© Jonessynthetic & Bartlett pollutants Learning, contaminating LLC the soil. Many NOT FOR SALEthe OR atmosphere. DISTRIBUTION NOT ofFOR these SALE microbes OR haveDISTRIBUTION been “domesticated” for this ▶ Consume 50% of the dead plant and animal very role through a process called bioremediation . matter generated on Earth each year. As new species are identifi ed and studied, the roles ▶ Operate as the engines that drive and control of the soil microbiome will be unraveled. nutrient and mineral cycling and that reg- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC ulate energy fl ow, both of which can affect The Atmosphere long-term climateNOT change.FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Viruses are the most abundant infectious More than 315 different types of bacteria have been agents on Earth. There are an estimated 10 31 viruses identifi ed in air masses 10 kilometers above the in the oceans and most of these viruses remain Earth’s surface. These microbes along with fungal uncharacterized. However, they probably infect spores account for 20% of all particles—biological and © Jones & Bartlett Learning, LLC non-biological—in© Jones the & Bartlettatmosphere Learning, ( FIGURE LLC1.1 C ). marineNOT microbes. FOR SALE Because OR many DISTRIBUTION of these microbes NOT FOR SALE OR DISTRIBUTION are important in the activities listed above, viruses Although less studied than the ocean and soil micro- undoubtedly play an infl uential role in the global biomes, scientists believe the atmospheric communi- cycling of nutrients and elements, such as carbon ties perform the following roles: and nutrients. In fact, infections by marine viruses ▶ Play an integral role with marine microbes © Jones &are Bartlett responsible Learning, for releasing LLC and recycling some© Jones & Bartlettin the formation Learning, of water LLC vapor (clouds).

NOT FOR150 SALE gigatons OR ofDISTRIBUTION carbon per year. NOT FOR▶ SALE Help form OR raindropsDISTRIBUTION and snowfl akes. Today, microbiologists around the world are ▶ Affect the chemical composition of the discovering many marine microbes that are new atmosphere. to science. What are the daily occupations of these ▶ Infl uence weather cycles, alter the com- and other mysterious microbes and viruses yet to position of rain and snow, and affect daily be identifi ed and cataloged?© Jones & Undoubtedly, Bartlett Learning, many LLC weather patterns.© Jones & Bartlett Learning, LLC play useful and probablyNOT intimate FOR SALE roles, OR the DISTRIBUTIONconse- Although we have muchNOT to FOR learn SALE and under-OR DISTRIBUTION quences of which we have yet to discover. The scien- stand about microbes in the clouds, it is evident that tifi c studies are just beginning. they help stabilize the atmosphere.

The Land The Earth’s Subsurface © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC MicrobesNOT on FOR dry SALEland are OR no lessDISTRIBUTION impressive in their Consider thatNOT the FOR oceans, SALE soil, OR and DISTRIBUTIONair represent only daily activities than their marine counterparts. In those environments most familiar to us. In fact, a fact, every time you walk on the ground, you step on diverse microbial workforce is being cataloged billions of microbes. Moreover, like their cousins in anywhere there is an energy source and water. For the oceans, they can be found in every imaginable example, scientists have drilled 2,400 meters into © Jones &place, Bartlett from theLearning, tops of the LLC highest mountains to the© Jonesthe Earth’s& Bartlett subsurface Learning, on land LLC or below the sea- NOT FORdeepest SALE caves.OR DISTRIBUTION In fact, a kilogram of moist gardenNOT ﬂFOR oor. In SALE the solid OR rock, DISTRIBUTION they have discovered another

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FIGURE 1.1 Daily Life in the Microbial World. Microbes play many roles. For example, (A) photosynthetic microbes inhabit the upper sunlit layer of almost all oceans and bodies of fresh water where they produce food molecules that sustain the aquatic food web and generate oxygen gas. (Bar = 20 μm.) © Jones & Bartlett Learning, LLC (B) In the soil, microbes© Jones degrade & Bartlett dead plants Learning, and animals, LLC form benefi cial partnerships with plants, and recycle carbon, nitrogen, and sulfur. (Bar = 5 μm.) NOT FOR SALE OR DISTRIBUTION NOT FOR(C) SALE Besides OR their DISTRIBUTION involvement in the formation of raindrops and snowfl akes, microbes in the atmosphere are important for water vapor to condense into clouds that help cool the Earth. (D) Large numbers of microbes can be found on and in the body where most play benefi cial roles for our health. (Bar = 2 μm.) (E) A few microbes have played disease roles and affected world health. This 1974 photo of a Bengali boy shows the effects of smallpox, which was responsible for 300–500 million deaths during the 20th century. »» What would © Jones &happen Bartlett to life onLearning, Earth if each LLCof the examples above ( A – D ) was© devoidJones of microbes?& Bartlett Learning, LLC NOT FOR(A) SALE © NNehring/E+/Getty OR Images. DISTRIBUTION (B) © Science Photo Library/Shutterstock. (C) © Loskutnikov/Shutterstock.NOT (D) ©FOR Science Photo SALE Library/Getty OR Images. DISTRIBUTION (E) Courtesy of Jean Roy/CDC.

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© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORfrontier SALE composedOR DISTRIBUTION of microbes that are sealed offNOT carryingFOR SALE out anOR amazing DISTRIBUTION array of metabolic reac- from the rest of the world. These intraterrestrials tions to help us resist disease, regulate our diges- (microbes living in sediment and rock) are another tion, maintain a strong immune system—and even diverse workforce that, even buried in rock, are infl uence our risk of obesity, asthma, and allergies. believed to make up more microbial biomass than To be human and healthy, we must share our daily that of all the microbes© Jones in water & andBartlett soil. Scientists Learning, LLClives with this homegrown© microbiome.Jones & Bartlett Learning, LLC believe these intraterrestrialsNOT FOR also SALE are involved OR DISTRIBUTION with One aspect of a microbe’sNOT daily FOR life SALE that we OR have DISTRIBUTION the daily recycling of minerals and stabilizing the overlooked until now is its role in infectious disease. biogeochemical health of our planet. This omission was done on purpose because only a very small minority of microbes are responsible for Today, © Jones the &workforce Bartlett Learning,composing LLCthe global infections© and Jones disease. & Although Bartlett such Learning, disease-causing LLC microbiome is still being cataloged and their num- agents, called pathogens, are rare, some, such as bers NOTand daily FOR activities SALE keepOR growing.DISTRIBUTION As Louis Pas- those causingNOT diseasesFOR SALE like ORplague, DISTRIBUTION malaria, and teur, one of the fathers of microbiology, once stated, smallpox ( FIGURE 1.1 E ), throughout history have “ Life [plant and animal] would not long remain possi- swept through cities and villages, devastated popula- ble in the absence of microbes.” tions, killed great leaders and commoners alike, and, © Jones & Bartlett That need Learning, for microbes LLC is evident even much© Jonesas a result, & Bartlett have transformed Learning, politics, LLC economies, and NOT FORcloser SALE to ORhome. DISTRIBUTION Microbial communities inhabit theNOT publicFOR SALEhealth onOR a DISTRIBUTIONglobal scale. Nevertheless, as you bodies of all plants and animals. For animals, most read through the chapters of this text, remember only every species, from termites to bees, from cows to a small minority of microbes are dedicated pathogens. humans, has an intimate microbiome associated A major focus of this introductory chapter is to with it. For example, the human microbiome con- give you an introspective “fi rst look” at microbiology— sists of some 40 trillion© Jones (40 × 10 &12 Bartlett ) microbes, Learning, which LLCthen and now. We will see© howJones microbes & Bartlett were fiLearning, rst LLC is about equal to theNOT number FOR ofSALE cells OR(30 DISTRIBUTION× 10 12 ) discovered and why infectiousNOT FORdisease SALE preoccupied OR DISTRIBUTION building the human body. These outwardly invisible the minds and efforts of so many. Along the way, we strangers have established themselves since birth will see how curiosity and scientifi c inquiry stimu- as separate and unique communities of microbes on lated the quest to understand the microbial world the skin, in the respiratory tract, and especially in just as the science of microbiology does today, as the gut© Jones(FIGURE & 1.1 Bartlett D). In fact, Learning, the human LLC gut micro- described ©in Jonesthe box MICROBIOLOGY& Bartlett Learning, PATHWAYS LLC. To biomeNOT is essential FOR SALE for a healthyOR DISTRIBUTION life. Although some begin our NOTstory, weFOR reach SALE back ORto the DISTRIBUTION 1600s, where we are transient, most of the species spend each day encounter some very inquisitive individuals.

Chapter Challenge © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONNow that you have learned a little about theNOT diverse FOR global SALE workforce OR ofDISTRIBUTION microorganisms, can you explain how the microbes were revealed and identify several challenges that some microorganisms pose for microbiology today? Let’s investigate!

Being a Scientist

Science © Jonesmight not & seem Bartlett like the Learning,most glamorous LLC profession. © Jones & Bartlett Learning, LLC In fact, as you read many of the chapters in this text, you mightNOT wonder FOR why SALEmany scientists OR DISTRIBUTION have the good fortune NOT FOR SALE OR DISTRIBUTION to make key discoveries. At times, it might seem like it is the luck of the draw, but actually many scientists share a set of characteristics that puts them on the trail to success. Robert S. Root-Bernstein, a physiology professor at Michigan © Jones &State Bartlett University, Learning, points out thatLLC many prominent scientists© Jones & Bartlett Learning, LLC NOT FORlike SALE to goof OR around, DISTRIBUTION play games, and surround themselvesNOT FOR SALE OR DISTRIBUTION © Comstock/Thinkstock. (continues)

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with a type of chaos aimed at revealing the unexpected. Their labs might appear to be in disorder, but they know exactly where every tube or bottle belongs. Scientists also identify intimately with the organisms or creatures they study (it is said that Louis Pasteur actually dreamed about microorganisms), and this identifi cation brings on an intuition—a “feeling for the organism.” In © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC addition, there is the abilityNOT to recognizeFOR SALE patterns OR that DISTRIBUTION might bring a breakthrough. (Pasteur hadNOT studied FOR art as SALE a teenager OR and DISTRIBUTION therefore had an appreciation of patterns.) The geneticist and Nobel laureate Barbara McClintock once remarked, “I was just so interested in what I was doing I could hardly wait to get up in the morning and get at it. One of my friends, a geneticist, said I was a child, because only children can’t wait to get up in the morning to get at what they want to do.” Clearly, another characteristic of a scientist is having a child-like curiosity© Jones for the unknown. & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Another NOT Nobel FOR laureate SALE and immunologist,OR DISTRIBUTION Peter Medawar, once said, “Scientists NOT are FOR people SALE of very ORdissimilar DISTRIBUTION temperaments doing different things in very different ways. Among scientists are collectors, classifi ers, and compulsive tidiers-up; many are detectives by temperament and many are explorers; some are artists and others artisans. There are poet-scientists and philosopher-scientists and even a few mystics.” In other words, scientists come from all lifestyles. For this author, I too have found science to be an extraordinary opportunity to discover and understand something never before © Jones &known. Science is fun, yet challenging—and at times arduous, tedious, and frustrating. As with most of us, we will not make Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORthe headlines for a breakthrough discovery or fi nd a cure for a disease. However, as scientists we all hope our hard work and SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION achievements will contribute to a better understanding of a biological (or microbiological) phenomenon and will push back the frontiers of knowledge and have a positive impact on society. Like any profession, being a scientist is not for everyone. Besides having a bachelor’s degree in biology or microbiology, you should be well read in the sciences and capable of working as part of an interdisciplinary team. Of course, you should have good quantitative and ©communication Jones & Bartlett skills, have Learning, an inquisitive LLC mind, and be goal oriented.© If Jonesall this sounds & Bartlett interesting, Learning, LLC maybe you fi t the mold of a scientist. Why not consider pursuing a career in microbiology? Some possibilities are described NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION in other MICROBIOLOGY PATHWAYS included in this text, but you should also visit with your instructor. Simply stop by the student union, buy two cups of coffee, and you are on your way.

KeY © Jones ConCept & Bartlett 1.1 Learning, The Discovery LLC of Microbes ©Leads Jones to &Questioning Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONTheir Origins NOT FOR SALE OR DISTRIBUTION

As the 17th century arrived, an observational revo- for the structure of cork. Seeing “a great many lit- lution was about to begin. A Dutch spectacle maker tle boxes,” he called these boxes cella (= rooms), and © Jones &named Bartlett Zacharias Learning, Janssen andLLC others discovered that if© Jonesfrom &that Bartlett observation Learning, today we LLC have the word “cell” NOT FORthey SALE combined OR DISTRIBUTION two curved lenses together, they couldNOT toFOR describe SALE the OR basic DISTRIBUTION unit of life. magnify small objects. Many individuals in Holland, Micrographia represents one of the most impor- England, and Italy further developed this combination tant books in science history. It awakened the of lenses that in 1625 would go by the term microsco- learned and general population of Europe to the world of the very small, revolutionized the art of pio or “microscope.” This© Jones new invention & Bartlett would Learning, be the LLC © Jones & Bartlett Learning, LLC forerunner of the modern-day instrument. scientifi c investigation, and showed that the micro- NOT FOR SALE OR DISTRIBUTIONscope was an importantNOT tool FOR for unlockingSALE OR the DISTRIBUTION Microscopy—Discovery of the Very Small secrets of an unseen world: the world of the cell. Robert Hooke, an English natural philosopher (the At this same time, across the North Sea in Delft, term “scientist” was not coined until 1833), was one Holland, Antoni van Leeuwenhoek, a successful of the© Jonesmost inventive & Bartlett and Learning,ingenious minds LLC in the tradesman© andJones dry &goods Bartlett dealer, Learning, was using LLC hand historyNOT of FORscience. SALE As the OR curator DISTRIBUTION of experiments lenses to NOTinspect FOR the SALEquality ORof his DISTRIBUTION cloth. As such, for the Royal Society of London, Hooke published a and without any scientifi c training, Leeuwenhoek book in 1665, called Micrographia , in which he took became skilled at grinding single pieces of glass into advantage of the magnifi cation abilities of the early fi ne magnifying lenses. Placing such a lens between microscopes to make detailed drawings of many two metal plates riveted together, Leeuwenhoek’s © Jones &living Bartlett objects, Learning, including LLC fl eas, lice, and peacock© Jones“simple & Bartlett microscope” Learning, could LLCgreatly out magnify NOT FORfeathers. SALE ORPerhaps DISTRIBUTION his most famous description wasNOT Hooke’sFOR SALE microscope OR DISTRIBUTION (FIGURE 1.2 A, B ).

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Specimen mount Screw plate © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Focusing screw © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Elevating screw

(A) (B) (C) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC FIGURE 1.2 Viewing Animalcules. (A) To view his animalcules, Leeuwenhoek placed his sample on the tip of the specimen NOT FORmount SALE that OR was DISTRIBUTION attached to a screw plate. An elevating screwNOT moved FOR the SALE specimen OR up DISTRIBUTIONor down, whereas the focusing screw pushed against the metal plate, moving the specimen toward or away from the lens. (B) Holding the microscope up to the bright light, Leeuwenhoek then looked through the lens to view his sample. (C) From such observations, Leeuwenhoek drew the animalcules he saw (bacteria in this drawing). »» Why would Leeuwenhoek believe his living (and often moving) creatures were tiny animals? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC (B) Collection of the University of MichiganNOT Health System, FOR Gift of SALE Pﬁ zer, Inc. (UMHS.15). OR (C)DISTRIBUTION © Royal Society, London. NOT FOR SALE OR DISTRIBUTION

Aware of Hooke’s Micrographia , Leeuwenhoek at the time found it diffi cult to repeat and verify his turned his microscope to the invisible world. Begin- observations, which also are key components of sci- ning in 1673 and lasting until his death in 1723, entifi c inquiry. Still, Leeuwenhoek’s observations of Leeuwenhoek© Jones communicated & Bartlett Learning, his microscope LLC obser- animalcules© Jonesopened & yet Bartlett a second Learning, door to another LLC vationsNOT through FOR moreSALE than OR 300 DISTRIBUTION letters to England’s entirely newNOT world: FOR the SALE world OR of the DISTRIBUTION microbe. Royal Society. In 1674, one of his fi rst letters described a sample of lake water. Placing the sample before his Do Animalcules Arise Spontaneously? lens, he described hundreds of tiny, moving particles In the early 1600s, most naturalists were vitalists , he thought were minute, living animals, which he individuals who thought life depended on a myste- © Jones &called Bartlett animalcules Learning, . In fact, LLC this discovery represents© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT riousFOR and SALE pervasive OR DISTRIBUTION “vital force” in the air. This force one of the most important observations in history provided the basis for the doctrine of spontaneous because Leeuwenhoek had described and illustrated generation , which suggested that some forms of life for the fi rst time the microbial world. In 1676, he could arise from nonliving, often decaying matter. mixed pepper with a previously collected sample of Others also embraced the idea, for they too wit- snow water. After three© weeks,Jones he & found Bartlett more Learning, animal- LLCnessed toads that appeared© Jonesfrom mud, & Bartlettsnakes com- Learning, LLC cules, including the fi rst unmistakable observations NOT FOR SALE OR DISTRIBUTIONing from the marrow of NOTa decaying FOR SALEhuman ORspine, DISTRIBUTION of bacteria (FIGURE 1.2 C). Among the other letters and rats arising from garbage wrapped in rags. sent to the Royal Society, he described all the differ- Resolving the reality of such bizarre beliefs ent types of microbes (except viruses) that we know would require a new form of investigation— of today. This included structural details of yeast cells, experimentation—and a new generation of experi- thread-like© Jones fungi, & andBartlett microscopic Learning, algae and LLC protozoa. mental naturalists© Jones arose. & Bartlett Learning, LLC TheNOT process FOR SALEof “observation” OR DISTRIBUTION is an important NOT FOR SALE OR DISTRIBUTION skill for all scientists and remains the cornerstone of all scientifi c inquiry. Hooke and Leeuwenhoek Redi’s Experiments are excellent examples of individuals with sound In 1668, the Italian naturalist Francesco Redi per- observational skills. Unfortunately, Leeuwenhoek formed one of history’s fi rst biological experiments. © Jones &invited Bartlett no one Learning, to work withLLC him, nor did he show© JonesAs described & Bartlett in INVESTIGATING Learning, LLC THE MICROBIAL NOT FORanyone SALE how OR heDISTRIBUTION made his lenses. Thus, naturalistsNOT WORLDFOR SALE 1, his ORexperiment DISTRIBUTION was designed to test the

9781284101041_CH01_001_034.indd 7 03/04/17 9:16 am 8 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

Can Life Arise Spontaneously? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC For centuries, many people,NOT FORlearned SALE and not, OR believed DISTRIBUTION that some forms of life could arise spontaneouslyNOT FOR fromSALE nonliving, OR DISTRIBUTION decaying matter. For example: OBSERVATION: In the 17th century, many people believed that fl y maggots (larvae) arose spontaneously from rotting meat. Francesco Redi set out to fi nd the answer. QUESTION:© Jones Do fly& maggotsBartlett arise Learning, spontaneously LLC from rotting meat? © Jones & Bartlett Learning, LLC HYPOTHESIS:NOT FOR Redi proposed that fl y maggots arise from hatched eggs laid in decaying meat by fl ies. If so, preventing SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION fl ies from laying eggs in the rotting meat should result in no maggots being generated. EXPERIMENTAL DESIGN: Redi obtained similar pieces of rotting meat and jars in which the meat would be placed. EXPERIMENT: One piece of meat was placed in an open jar, whereas the other piece was placed in a similar jar that was © Jones & then covered with a piece of gauze to keep out any fl ying insects, including fl ies. The meat in each jar was allowed to rot. Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE RESULTS: OR See fi gure. DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Rotting allowed to occur © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Open jar Covered jar

CONCLUSIONS: © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC QUESTION 1: From Redi’s experiments, was his hypothesis validated? Explain using the ﬁ gure. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION QUESTION 2: What is the control in this experiment, and why was it important to have a control? QUESTION 3: Why was it important that Redi used gauze to cover the one jar and not seal it completely? Hint: Remember what people believed about the “vital force.” You can fi nd answers online in © Jones & Bartlett Learning,Appendix E . LLC © Jones & Bartlett Learning, LLC ModiﬁNOT ed from Redi, FOR F. 1688. AsSALE reprinted by OpenOR Court DISTRIBUTION Publishing Company, Chicago (1909). NOT FOR SALE OR DISTRIBUTION

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© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORbelief SALE that OR worm-like DISTRIBUTION maggots (fl y larvae) couldNOT conclusionsFOR SALE and OR suggestedDISTRIBUTION that the animalcules arise spontaneously from rotting meat. came from the air and would therefore grow in the Although Redi’s experiments verifi ed that spon- broth of the cooled fl asks. To validate his claim, in taneous generation did not produce larger living 1765, he repeated Needham’s experiments by boil- creatures like maggots, what about the mysteri- ing fl asks with broth for an extended time before ous and microscopic© animalcules Jones & Bartlett that appeared Learning, to LLCsealing some fl asks. After© Jones 2 days, & the Bartlett broths Learning, in LLC straddle the boundaryNOT between FOR SALEthe nonliving OR DISTRIBUTION and the open fl asks were swarmingNOT FOR with SALE animalcules, OR DISTRIBUTION living world? Could they arise spontaneously? whereas the sealed ones contained no animalcules. Spallanzani concluded that microbes from the air, Needham’s Experiments and not spontaneous generation, accounted for the © Jones & Bartlett Learning, LLC presence of© animalculesJones & Bartlett in the fl asks.Learning, LLC In 1745, a British clergyman and naturalist, John The controversy over spontaneous generation of Needham,NOT FORproposed SALE that OR the DISTRIBUTION spontaneous genera- animalculesNOT continued FOR SALE into the OR mid-1800s DISTRIBUTION and only tion of animalcules resulted from a vital force that deepened when Rudolf Virchow, a German patholo- reorganized decaying matter into life. Needham pre- gist, put forward, without direct evidence, the idea sented experiments showing that animalcules could of biogenesis, which said that life arises only from arise spontaneously in fl asks of animal broth that © Jones & Bartlett Learning, LLC © Joneslife. To& solveBartlett the debateLearning, concerning LLC microbial spon- previously had been heated and then kept at room NOT FOR SALE OR DISTRIBUTION NOT taneousFOR SALE generation, OR DISTRIBUTION a new experimental strategy temperature for several days. He was convinced that would be needed. the vital force provided the stimulus needed for spontaneous generation. Pasteur’s Experiments Louis Pasteur, a French chemist and scientist, took Spallanzani’s Experiments© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC up the challenge of spontaneous generation, and in NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Experiments often can be subject to varying inter- 1861 he designed an elegant series of experiments pretations. As such, the Italian cleric and natu- that were a variation of the methods of Needham ralist Lazzaro Spallanzani challenged Needham’s and Spallanzani. The box MICROINQUIRY 1 outlines

MICROINQUIRY 1 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE Scientiﬁ OR c InquiryDISTRIBUTION and Spontaneous GenerationNOT FOR SALE OR DISTRIBUTION Science is a systematic way of thinking and learning about that organisms do not appear from nonliving matter but the natural world. Often we accept and integrate into our rather from the air in which they are located. understanding new information because it appears con- Question: Next comes the question, which can be asked sistent with what we believe is true. But, are we sure our in many ways but usually as a “what,” “why,” or “how” ideas are always correct?© Jones In science, & Bartlett scientiﬁ c inquiryLearning, , or LLCquestion. For example, “What accounts for the generation © Jones & Bartlett Learning, LLC what has been called the “scientifi c method,” is a way to NOT FOR SALE OR DISTRIBUTIONof microorganisms in the animal broth?” NOT FOR SALE OR DISTRIBUTION examine those ideas. Hypothesis: A hypothesis is a provisional but testable Scientifi c inquiry often uses deductive reasoning , which explanation for an observed phenomenon or observation. begins with general observations, builds a hypothesis, Pasteur’s hypothesis was that “Organisms appearing in carries out well-designed and carefully executed exper- the sterile fl ask come from other organisms in the air.” If iments © Jones to test & the Bartlett hypothesis, Learning, and reaches LLC a specifi c, so, air allowed to enter the sterile fl ask will contain organ-© Jones & Bartlett Learning, LLC logical conclusion. Pasteur used this inquiry approach in isms that will grow in such profusion that they will be 1861NOT to test FOR the ideaSALE of spontaneous OR DISTRIBUTION generation of micro- seen as a cloudyNOT liquid.FOR SALE OR DISTRIBUTION organisms. Let’s see how it worked: Let’s analyze the experiments. In Pasteur’s experimen- Observations: When studying a problem, the inquiry tal design, only one variable (an adjustable condition) process usually begins with observations. For spontane- changed. In the accompanying fi gure, one fl ask remained ous generation, Pasteur’s earlier observations suggested intact, whereas two others were exposed to the air by © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC (continues) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

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Scientiﬁ c Inquiry© andJones Spontaneous & Bartlett Learning,Generation LLC © Jones & Bartlett Learning, LLC ( A) breaking the neckNOT or ( B ) tipping the fl ask. Pasteur kept FOR SALE OR DISTRIBUTIONappeared in the intact fl ask is interesting but tells us very NOT FOR SALE OR DISTRIBUTION all other factors the same; that is, all of the broths were little by itself. Its signifi cance comes by comparing it to heated and cooled for the same length of time, and the the broken neck fl ask and tipped fl ask where organisms fl asks were identical. Thus, the experiments had a rigor- quickly appeared. ous control (the comparative condition wherein the fl ask Conclusion: Pasteur’s hypothesis was supported by the remained © Jones intact). & Bartlett Pasteur’s fi nding Learning, that LLC no organisms experiments.© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION General When studying a problem, the inquiry process usually begins with observations. For spontaneous generation, observations Pasteur’s earlier observations suggested that organisms do not appear from nonliving matter but rather from the air in which they are located.

Question Next comes the question, which can be asked in many ways but usually as a “what,” “why,” or “how” question. © Jones & Bartlett Learning,For exampl LLCe, “What accounts for the appearance© Jones of microo &rga Bartlettnisms in the Learning,animal broth?” LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Hypothesis A hypothesis is a provisional but testable explanation for the question or observation. Pasteur’s hypothesis was that “Organisms appearing in the sterile flask come from other organisms in the air.” If so, then air allowed to enter the sterile flask will contain organisms that will grow in such profusion that they will be seen as a cloudy liquid.

Swan-necked flask Experiments © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTDust and FOR SALE OR DISTRIBUTION microorganisms Air Flask Time are trapped cooled passes enters

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONSterile broth NOTNo FOR organisms SALE OR DISTRIBUTION The experiment appear begins with a boiled (A) (B) broth solution similar Flask neck Flask tilted so to that of Needham snapped off broth enters neck Time and Spallanzani. passes © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Specific results Organisms appear Organisms appear

Pasteur and the Spontaneous Generation Controversy. If broth sterilized in a swan-necked fl ask is left open to the air, the curvature of the neck traps dust particles and microorganisms, preventing them from reaching the broth. However, if the neck is snapped off to allow in air or the fl ask is tipped so broth enters the neck, organisms encounter the broth and© grow.Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the process of scientiﬁ c inquiry and Pasteur’s in spontaneous generation and validated the idea of experiments. biogenesis. Although Pasteur’s experiments generated con- Today there is another form of “spontaneous © Jones &siderable Bartlett debate Learning, for several LLC years, his exacting and© Jonesgeneration” & Bartlett occurring—this Learning, LLCtime in the research NOT FORcarefully SALE ORdesigned DISTRIBUTION experiments disproved the beliefNOT laboratory,FOR SALE as ORMICROFOCUS DISTRIBUTION 1. 1 relates.

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Generating Life—Today © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Those who believed inNOT spontaneous FOR SALE generation OR proposedDISTRIBUTION that animalcules arose from the rearrangementNOT FOR SALE of molecules OR DISTRIBUTION released from decayed organisms. Although this idea for the generation of life was incorrect, today we are getting closer to generating new life by rearranging molecules in the laboratory. In 2002, scientists at the State University of New York, Stony Brook, reconstructed a poliovirus by assembling separate poliovirus genes and proteins. A year later, Craig Venter and his group assembled a bacteriophage—a virus that infects bacterial cells—from “off-the-shelf” biomolecules. Then, in 2010, © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC another team, again led by Venter, synthesized from scratch theNOT complete FOR genetic SALE sequence OR DISTRIBUTION of the bacterium Mycoplasma NOT FOR SALE OR DISTRIBUTION mycoides and inserted the sequence into a cell of Mycoplasma capricolum from which its genetic information previously had been removed (see fi gure). This “new organism” now functioned like an M . mycoides cell. © Jones & Bartlett However, this is not “generating new life.” Rather, it is putting Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEa new setOR of DISTRIBUTION genes into another cell that never beforeNOT had FOR SALE OR DISTRIBUTION that set of genes. This new fi eld of biology is called synthetic biology , and it aims to rebuild or create new “life forms” (such as bacterial cells) from scratch by recombining molecules taken from other organisms. It is like fashioning a new car by taking various parts ©from Jones a Ford & and Bartlett Chevy and Learning, assembling LLC © Jones & Bartlett Learning, LLC them on a Toyota chassis. Why do this? The designNOT and FOR construction SALE ofOR novel DISTRIBUTION organisms, NOT FOR SALE OR DISTRIBUTION having functions very different from naturally occurring organisms, present the opportunity to expand evolution’s repertoire by fabricating cells that are better at doing specifi c jobs. Can we, for example, design bacterial cells that are better© Jonesat degrading & Bartlett toxic wastes, Learning, providing LLCalternative energy © Jones & Bartlett Learning, LLC sources,NOT or FOR making SALE cheaper OR pharmaceuticals? DISTRIBUTION These and many A false-colorNOT electron FOR SALE microscope OR image DISTRIBUTION of synthetic other positive benefi ts are envisioned as outcomes of synthetic Mycoplasma cells. (Bar = 1 μm.) biology and the generation of new life. © Thomas Deerinck, NCMIR/Science Source.

a. How were the fi rst microbes discovered? b. If you were alive in Leeuwenhoek’s time, how would you explain the origin for the animalcules he saw with his simple microscope? c. Evaluate the role© of Jonesexperimentation & Bartlett as an importantLearning, skill LLCto the eventual rejection of spontaneous© Jones generation & Bartlett as an Learning, LLC origin for animalculesNOT (and FOR microbes). SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

KeY ConCept 1.2 Disease Transmission Can Be Prevented © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION In the 13th century, people knew diseases could be contagious, disﬁ guring, and often deadly disease that transmitted between individuals, so they enforced affected humans. In an effort to prevent individuals isolations, called quarantines , in an attempt to pre- from contracting smallpox, the Chinese practiced vent disease spread. Other interventions to prevent variolation, which involved blowing a ground small- © Jones &infection Bartlett can Learning, be traced back LLC to the 14th century. At© Jonespox powder & Bartlett into theLearning, nose of individuals. LLC By the 18th NOT FORthat SALE time, OR and DISTRIBUTION throughout history, smallpox was aNOT century,FOR SALE Europeans OR DISTRIBUTION were inoculating dried smallpox

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© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORscabs SALE under OR theDISTRIBUTION skin of the arm. Although someNOT FOR SALE OR DISTRIBUTION individuals did get smallpox, most contracted only Leather hat (indicating a mild form of the disease and, upon recovery, were a doctor) protected against subsequent smallpox exposures. Mask with glass eyes © Jones & Bartlett Learning, LLC © Jonesand & beakBartlett containing Learning, a LLC Vaccination Prevents the Spread of Smallpox “protective” perfumed NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION In the late 1700s, smallpox epidemics were preva- sponge lent throughout Europe. In England, smallpox epi- Stick to remove clothes demics were so severe that one-third of the children of a plague victim died before the age of three and many victims who recovered© Jones often & were Bartlett blinded Learning, and left pockmarked. LLC © Jones & Bartlett Learning,Gloves LLC As NOT an EnglishFOR SALE country OR surgeon, DISTRIBUTION Edward Jenner NOT FOR SALE OR DISTRIBUTION learned that milkmaids who occasionally contracted Waxed linen robe a mild disease called cowpox would subsequently be protected from contracting smallpox. Because cow- Boots pox was not deadly, Jenner hypothesized that inten- © Jones &tionally Bartlett giving Learning, cowpox LLCto people should protect© Jones & Bartlett Learning, LLC NOT FORthem SALE against OR DISTRIBUTIONsmallpox. In 1796, he took a scrapingNOT FOR SALE OR DISTRIBUTION of a cowpox blister from a milkmaid’s hand and FIGURE 1.3 Dressed for Protection. This dress was scratched it into the skin of a young boy’s arm. The thought to protect a plague doctor from the air (miasma) boy soon developed a slight fever but recovered. Six that caused the plague. »» How would each item of dress offer protection? weeks later, Jenner infected the boy with smallpox pus. Within days, the© Jonesboy developed & Bartlett a reaction Learning, at LLCCourtesy of National Library of Medicine. © Jones & Bartlett Learning, LLC the skin site but failedNOT to show FOR any SALE sign ofOR smallpox. DISTRIBUTION NOT FOR SALE OR DISTRIBUTION In 1798, Jenner repeated his experiments with poisonous particles of rotting matter expelled into others, verifying his technique of vaccination (vacca the air (the word “malaria” comes from mala aria , = “cow”). Prominent physicians soon confi rmed his meaning “bad air”). To protect oneself from the fi ndings,© Jones and within & Bartlett a few Learning, years, Jenner’s LLC method black plague,© Jones for example, & Bartlett plague Learning, doctors in EuropeLLC often wore an elaborate costume they thought would of vaccinationNOT FOR spread SALE through OR DISTRIBUTION Europe and abroad. NOT FOR SALE OR DISTRIBUTION However, it would not be until 1980, some 284 years protect them from the plague miasma (FIGURE 1.3 ). after Jenner’s fi rst smallpox vaccinations, that the As the 19th century unfolded, more scientists World Health Organization (WHO) would certify were relying on keen observations and experimenta- that smallpox had been eradicated globally through tion as a way of understanding and explaining disease © Jones &a massiveBartlett vaccination Learning, effort LLC that was carried out© Jonestransmission—and & Bartlett Learning, challenging LLC the idea of miasmas. NOT FORbetween SALE 1966OR DISTRIBUTION and 1979. NOT FOREpidemiology SALE OR, DISTRIBUTIONas applied to infectious diseases, In retrospect, it is remarkable that without any is another example of scientifi c inquiry—in this case knowledge of microbes or disease causation, Jenner to identify the source, cause, and mode of trans- accomplished what he did. Again, hallmarks of a mission of disease within populations. The fi rst scientist—keen observational skills and insight—led such epidemiological studies, carried out by Ignaz to a therapeutic intervention© Jones &against Bartlett disease. Learning, His LLCSemmelweis and John Snow,© Jones were instrumental& Bartlett Learning, in LLC work, along with others,NOT wouldFOR SALElay the ORfoundation DISTRIBUTION suggesting how diseases wereNOT transmitted FOR SALE and OR how DISTRIBUTION for the fi eld of immunology , the study of the body’s simple measures could prevent transmission. defenses against, and responses to, foreign organisms and substances. Semmelweis and “Cadaver Matter” Ignaz Semmelweis was a Hungarian obstetrician Disease © Jones Transmission & Bartlett Does Learning, Not Result LLC from © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION who, at theNOT age FOR of 29, SALE was ORappointed DISTRIBUTION chief resi- a Miasma dent at a large maternity hospital in Vienna, Aus- So, the question remains. What causes infectious tria. Soon after his arrival, he was shocked by the disease? In the 1700s, the prevalent belief among numbers of women in his ward who were dying of naturalists and laypersons alike was that disease childbed fever (a type of blood poisoning also called © Jones &resulted Bartlett from Learning, a miasma , LLCwhich was thought to arise© Jonespuerperal & Bartlett fever) followingLearning, labor. LLC The box CLINICAL NOT FORfrom SALE a foul OR quality DISTRIBUTION of the atmosphere or from tinyNOT CASEFOR SALE1 outlines OR Semmelweis’DISTRIBUTION investigations into

9781284101041_CH01_001_034.indd 12 03/04/17 9:16 am KEY CONCEPT 1.2 Disease Transmission Can Be Prevented 13

Childbed Fever: A Historical Reflection © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC In 1844–1846, manyNOT mothers FOR SALE in 20OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the First Maternity Division of the Vienna hospital first maternity division Vienna General Hospital, which was Vienna hospital second maternity division run by doctors and medical students, contracted a serious disease called 15 childbed© Jones fever &(puerperal Bartlett fever). Learning, Up r LLC © Jones & Bartlett Learning, LLC to 11% of the mothers died from theNOT illness. FOR However, SALE in the OR adjacent DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Second Maternity Division of the same hospital run by midwives, the death toll from childbed fever was 10 less than 3% over the same period. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC As a member of the medical staff of

NOT FOR SALEthe First OR Division, DISTRIBUTION Ignaz Semmelweis Childbed Feve Deaths, rcent NOT FOR SALE OR DISTRIBUTION searched for an explanation for the Pe high mortality in his division. 5 Most of the medical staff attributed the illnesses and deaths© Jones of puerperal & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC fever to an unavoidable miasma. Semmelweis discountedNOT this FOR belief SALE OR0 DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

because how could one reconcile the 1800 1802 1804 1806 1808 1810 1812 1814 1816 1818 1820 1822 1824 1826 1828 1830 1832 1834 1836 1838 1840 1842 1844 1846 1848 fact that while the fever was raging in the First Division, few cases occurred Yearly Mortality for Childbed Fever 1800–1849. Semmelweis collected data in the Second Division, and hardly a on deaths of birthgiving mothers in the Vienna maternity hospital (red line) and case© occurredJones in& the Bartlett surrounding Learning, city compared LLC the deaths to those in the© Jones second maternity& Bartlett division Learning, where midwives LLC of Vienna?NOT FOR SALE OR DISTRIBUTIONfocused on attending to births andNOT did not FOR concern SALE themselves OR DISTRIBUTION with anatomical Others attributed the fever to pathology. »» Why do Semmelweis’ observations on the prevalence of childbed fever overcrowding in the First Division. not support a miasma as the cause of and transmission for the disease?

Semmelweis pointed out that, in Data from Semmelweis (1861). fact, the crowding was heavier in the © Jones & SecondBartlett Division. Learning, In addition, LLC there were no differences between© Jones the &two Bartlett divisions Learning,with regard to LLC diet, general care, and NOT FOR SALEmethod ORof examination DISTRIBUTION of maternity patients. NOT FOR SALE OR DISTRIBUTION In 1847, Jakob Kolletschka, professor of forensic medicine in the hospital and a colleague of Semmelweis, was instructing medical students in the art of medical dissection of cadavers in the morgue (deadhouse). While performing an autopsy, Kolletschka punctured a fi nger with a bloody scalpel. He ended up dying from the infection and Semmelweis observed that Kolletschka exhibited the same symptoms as the victims of childbed fever. Semmelweis also noted© Jonesthat (a) in & the Bartlett Second Division, Learning, the midwives LLC neither received anatomical© Jones instruction & Bartlett nor did they Learning, LLC dissect cadavers in the deadhouse; (b) he and his medical students examined women in labor in the First Division without NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION cleaning up after performing their dissections in the deadhouse (see fi gure). Questions: a. How was the childbed fever illness transmitted to Professor Kolletschka? b. From Semmelweis’ observations, what was the source of childbed fever? c.© Why Jones was the & incidenceBartlett of Learning, the disease so LLC low in the Second Division? © Jones & Bartlett Learning, LLC d.NOT How wasFOR the SALE agent of OR childbed DISTRIBUTION fever transmitted to maternity patientsNOT in the FORFirst Division? SALE OR DISTRIBUTION You can fi nd answers online in Appendix E . For additional information, read The Doctors’ Plague: Germs, Childbed Fever, and the Strange Story of Ignác Semmelweis by Sherwin B. Nuland. (New York: W.W. Norton & Company. 2004.) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 13 03/04/17 9:16 am 14 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORthe SALE source OR and DISTRIBUTION mode of transmission of the dis-NOT FOR SALE OR DISTRIBUTION ease and the intervention he introduced to stop the transmission of childbed fever. After Semmelweis directed his staff to wash their hands in chlorine water before entering the maternity ward, deaths© Jones from childbed & Bartlett fever Learning, imme- LLC © Jones & Bartlett Learning, LLC diately plummeted. NOTSemmelweis FOR SALE believed OR “cadaver DISTRIBUTION NOT FOR SALE OR DISTRIBUTION matter” on the hands of the staff doctors was the agent of disease and its transmission could be inter- rupted by hand washing. Unfortunately, few physicians© initially Jones heeded& Bartlett Semmelweis’ Learning, measures LLC and © Jones & Bartlett Learning, LLC he was relieved of his position in 1849. It is believed that heNOT might FOR have SALE died inOR 1865 DISTRIBUTION from the very infec- NOT FOR SALE OR DISTRIBUTION tious agent he had studied.

Snow and “Organized Particles” © Jones &In Bartlett1854, a choleraLearning, epidemic LLC hit London’s Soho© Jones & Bartlett Learning, LLC NOT FORdistrict. SALE WithOR DISTRIBUTION many residents dying, English sur-NOT FOR SALE OR DISTRIBUTION geon John Snow carried out one of the first thor- ough epidemiological studies to discover how this acute intestinal infection was spread. By inter- viewing sick and healthy© Jones Londoners & Bartlett and Learning,plotting LLC © Jones & Bartlett Learning, LLC the location of each cholera case on a district map NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (FIGURE 1.4), Snow discovered that most cholera cases were linked to a sewage-contaminated FIGURE 1.4 Blocking Disease Transmission. John Snow water pump on Broad Street from which numer- (inset) produced a map plotting all the cholera cases (black rectangles) in the London Soho district and observed a cluster ous local residents obtained their household (circle) near the Broad Street pump (red arrow). »» Why would drinking© Jones water. & Bartlett Learning, LLC removing the ©pump Jones handle &stop Bartlett the spread Learning, of cholera? LLC Although Snow did not know the cause of chol- NOT FOR SALE OR DISTRIBUTION Courtesy of Frerichs, R.NOT R. John Snow FOR website: SALEhttp://www.ph.ucla.edu/epi/snow.html, OR DISTRIBUTION 2006. Inset courtesy era, he hypothesized that the Broad Street water of National Library of Medicine. pump was the source of the infectious agent. Snow instituted the fi rst known example of a public health measure to prevent disease transmission—he © Jones &requested Bartlett the Learning, parish Board LLC of Guardians to remove© Jones The Stage& Bartlett Is Set Learning, LLC NOT FORthe SALE handle OR from DISTRIBUTION the Broad Street pump! CholeraNOT DuringFOR SALE the early OR yearsDISTRIBUTION of the 1800s, other events cases dropped and again disease spread was broken occurred that helped set the stage for the coming by a simple procedure. “germ revolution.” In the 1830s, advances were Similar to Semmelweis’ cadaver matter, Snow made in microscope optics that allowed better res- believed “organized particles” in the water caused olution of objects. This resulted in improved and cholera; this was another© Jones hypothesis & Bartlett that proved Learning, to LLCmore widespread observations© Jones of tiny & livingBartlett organ- Learning, LLC be correct even thoughNOT the FOR causative SALE agent OR DISTRIBUTIONwould isms, many of which resembledNOT FORshort SALEsticks. InOR fact, DISTRIBUTION not be identifi ed for another 29 years. in 1838 the German biologist Christian Ehrenberg It is important to realize that although the suggested these “rod-like” looking organisms be miasma premise was incorrect, the fact that dis- called bacteria (bakter = “rod”). To understand clearly the nature of infectious ease© was Jones associated & Bartlett with bad Learning, air and fi lth LLC led to new © Jones & Bartlett Learning, LLC hygiene measures, such as cleaning streets, laying disease, a new concept of disease had to emerge. In new NOTsewer FOR lines SALEin cities, OR and DISTRIBUTION improving working doing so, NOTit would FOR be necessarySALE OR to DISTRIBUTIONdemonstrate that conditions. These changes helped usher in the San- a specifi c infectious disease was caused by a specifi c itary Movement and create the infrastructure for “germ.” This would require some very insightful the public health systems we have today, which is a work, guided by Louis Pasteur in France and Robert © Jones &team Bartlett effort explainedLearning, in LLC MICROFOCUS 1.2 . © JonesKoch & in Bartlett Germany. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 14 03/04/17 9:16 am KEY CONCEPT 1.2 Disease Transmission Can Be Prevented 15

Epidemiology—Today © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC On September 2, 2011,NOT the ColoradoFOR SALE Department OR DISTRIBUTIONof Public Health and Environment reportedNOT an abnormally FOR SALE high number OR DISTRIBUTION of people admitted to local hospitals suffering from fever and muscle aches as well as diarrhea or other gastrointestinal symptoms. Doctors quickly diagnosed the illness as a bacterial infection caused by Listeria monocytogenes . In the footsteps of Semmelweis and Snow, today’s health experts needed to locate rapidly the source and transmission mechanism of this outbreak. This often requires an entire team of medical investigators, including those from the Centers for ©Disease Jones Control & Bartlett and Prevention Learning, (CDC), state LLC and local health departments,© Jones and the & Coordinated Bartlett OutbreakLearning, Response LLC and Evaluation (CORE) Network, which is part of the Food and Drug Administration (FDA). See fi gure. ForNOT this FORoutbreak, SALE the CORE OR team DISTRIBUTION was made up of epidemiologists, microbiologists,NOT FOR health SALE specialists, OR DISTRIBUTION consumer safety oﬃ cers, and policy analysts. The CORE surveillance team confi rmed that Listeria was the infectious agent, while the response team identifi ed locally grown Listeria -contaminated whole cantaloupes as the source of the outbreak. They then issued a national warning, as the number of cases had expanded beyond Colorado. © Jones & BartlettAfter the Learning, outbreak, theLLC CORE post-response team© Jones & Bartlett Learning, LLC NOT FOR SALEdiscovered OR that DISTRIBUTION the farm growing the cantaloupes had failedNOT FOR SALE OR DISTRIBUTION to follow safe food-handling practices in the facility where the whole cantaloupes were stored and packed for shipment. The farm also failed to adequately clean the processing equipment, which had been used incorrectly, leading to the contamination. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Even with this rapid response, the Listeria cantaloupe contamination was theNOT deadliest FOR foodborne SALE diseaseOR DISTRIBUTION outbreak NOT FOR SALE OR DISTRIBUTION in the United States in nearly 90 years, killing 30 people and sickening 146 in 28 states. Unlike the time of Semmelweis and Snow, today’s potential for disease spread requires numerous response teams with the expertise and know- how© like Jones CORE. & With Bartlett an ever-present Learning, danger LLC of emerging © Jones & Bartlett Learning, LLC A group of FDA medical investigators form a Coordinated disease, epidemiology today is a team effort that remains a NOT FOR SALE OR DISTRIBUTION Outbreak ResponseNOT FOR and Evaluation SALE OR(CORE) DISTRIBUTION team. critical tool in the fi ght against infectious disease. Courtesy of FDA.

a. How do the procedures of variolation and vaccination contradict the concept of miasmas? b. How did the work© of Jones Semmelweis & Bartlett and Snow Learning, challenge the LLC widely held idea of miasmas© as Jones the cause & Bartlettof infectious Learning, LLC disease? NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

© Jones Chapter& Bartlett Challenge Learning, A LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION We are beginning to see how microbes and pathogens were discovered through the observations and studies of natural philosophers, a vaccine pioneer, and the fi rst epidemiologists. QUESTION A: What three infectious diseases described in this section were thought to be caused by a miasma? What types of studies and actions suggested these diseases were not the product of a miasma? © Jones & You can fi nd the answers online in Bartlett Learning, LLC Appendix F . © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 15 03/04/17 9:16 am 16 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

Beginning around 1854, the association of microbes alcohol. Fermentation, then, was a biological process with the disease process blossomed. Over the next and yeasts were living agents responsible for fer- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 60 years, the foundations would be laid for the mentation. maturing process thatNOT has FOR led toSALE the modernOR DISTRIBUTION sci- Pasteur also demonstratedNOT thatFOR wines, SALE beers, OR and DISTRIBUTION ence of microbiology. This period is referred to as vinegar each contained different and specifi c types the fi rst, or classical, Golden Age of microbiology. of microorganisms that had specifi c properties. For example, in studying a local problem of wine souring, Louis Pasteur Proposes That Germs Cause he observed that only the soured wines contained Infectious© Jones Disease & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION populationsNOT of bacterial FOR SALE cells (ORFIGURE DISTRIBUTION 1.5 B). Pasteur Trained as a chemist, Louis Pasteur (FIGURE 1.5 A ) concluded that these cells must have contaminated was among the fi rst scientists who believed that a batch of yeast and, as another example of a bio- problems in science could be solved in the labora- logical process, produced the acids that caused the tory with the results having practical applications. souring. Pasteur recommended a practical solution © Jones & Bartlett Always one Learning, to tackle LLCbig problems, Pasteur soon© Jonesfor the & “wineBartlett disease” Learning, problem: LLC heat the wine gently NOT FORset SALE out to OR understand DISTRIBUTION the chemical process of fer-NOT toFOR kill theSALE harmful OR bacterialDISTRIBUTION cells but not so strongly mentation. The prevailing theory in the 1850s held as to affect the quality of the wine. His controlled that fermentation was strictly a chemical process heating technique, which would become known as and the yeasts needed for fermentation were sim- pasteurization , soon was applied to other products. ply inert chemical “globules” catalyzing the pro- Today, pasteurization is a universal method used to cess. Pasteur’s microscope© Jones observations, & Bartlett however,Learning, LLCkill pathogens and retard ©spoilage Jones in & milk Bartlett and many Learning, LLC consistently revealedNOT large FOR numbers SALE of OR tiny DISTRIBUTION yeast other foods and beverages.NOT FOR SALE OR DISTRIBUTION cells in fermented juice. When he mixed yeast If wine disease was caused by tiny, living bacte- in a sugar-water solution in the absence of air, ria, Pasteur reasoned that human infections and dis- the yeast multiplied and converted the sugar to ease also might be caused by other microorganisms © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

FIGURE 1.5 Louis Pasteur and Fermentation Bacteria. (A ) Louis Pasteur as a 46-year-old professor of chemistry at the Uni- versity of Paris. (B) A drawing of some of the bacterial cells Pasteur observed in soured wine. »» Why would such cells exist in © Jones &a wine Bartlett bottle that Learning, had soured? LLC © Jones & Bartlett Learning, LLC NOT FORCourtesy SALE of National OR Library DISTRIBUTION of Medicine. NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 16 03/04/17 9:16 am KEY CONCEPT 1.3 The Classical Golden Age of Microbiology Reveals the Germ 17

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORin SALE the environment—what OR DISTRIBUTION he called germs. Thus,NOT Therefore,FOR SALE germs OR can DISTRIBUTION come from the environment— Pasteur formulated the germ theory of disease , and they can be controlled. which held that some microorganisms are responsible for infectious disease. Silkworm Disease and Cholera The Work of Lister© andJones Pasteur & Bartlett Stimulate Learning, LLCBetween 1857 and 1878, ©Pasteur Jones sought & Bartlett more evi-Learning, LLC Disease Control andNOT Reinforce FOR SALE OR DISTRIBUTIONdence for his germ theoryNOT idea. FOR In SALE1865, Pasteur OR DISTRIBUTION the Germ Theory had the opportunity to study pébrine, an infectious disease of silkworms. After several setbacks and Pasteur had reasoned that if germs were acquired 5 years of work, he fi nally identifi ed a new type of from the environment, their spread could be con- germ, unlike the bacterial cells and yeast he had trolled© Jonesand the &chain Bartlett of disease Learning, transmission LLC bro- © Jones & Bartlett Learning, LLC observed with his microscope. These tiny germs, ken, as Semmelweis and Snow had shown years NOT FOR SALE OR DISTRIBUTION which he NOTcalled FOR “corpuscular SALE OR parasites”, DISTRIBUTION were the earlier. infectious agent in silkworms and on the mulberry leaves fed to the worms. By separating the healthy Lister and Antisepsis silkworms from the diseased silkworms and their © Jones & Hearing Bartlett of Pasteur’sLearning, germ LLC theory, Joseph Lister, a© Jonescontaminated & Bartlett food, Learning, he managed LLC to quell the spread NOT FORprofessor SALE OR of surgery DISTRIBUTION at Glasgow Royal Infi rmary inNOT ofFOR the SALE silkworm OR disease. DISTRIBUTION The identifi cation of the Scotland, wondered if germs were responsible for pathogen was crucial to supporting the germ the- the large number of postoperative infections among ory, and Pasteur would never again doubt the ability his amputation patients. So, in 1865, knowing that of germs to cause infectious disease. carbolic acid had been effective on sewage control, Also in 1865, cholera engulfed Paris, killing 200 Lister used a carbolic© acidJones spray & Bartlettin surgery Learning, and on LLCpeople a day. Determined ©to Jonesfi nd the &causative Bartlett agent, Learning, LLC surgical wounds ( FIGURENOT FOR 1.6). SALEThe results OR DISTRIBUTION were Pasteur tried to capture theNOT responsible FOR SALE germ ORby fi DISTRIBUTIONl- spectacular—the wounds healed without infection tering the air around hospitalized patients and trap- in almost 70% of his cases. His technique would ping the germs in cotton. Unfortunately, Pasteur soon not only revolutionize medicine and the could not grow or separate one type of germ from oth- practice of surgery but also lead to the practice of ers because his broth cultures allowed all the organ- antisepsis© Jones, the &use Bartlett of chemical Learning, methods LLC for disin- isms on the© cottonJones to & mix Bartlett freely. To Learning, validate the LLC germ fectionNOT of externalFOR SALE living OR surfaces, DISTRIBUTION such as the skin. theory, whatNOT was FOR missing SALE was ORthe abilityDISTRIBUTION to isolate a

FIGURE 1.6 Lister and Antisepsis. Joseph Lister (inset) and his students used a carbolic acid spray in surgery and on surgi- © Jones &cal Bartlett wounds to Learning,prevent postoperative LLC infections. »» Hypothesize© Jones how carbolic & Bartlett acid prevented Learning, surgical infections. LLC NOT FORMary SALE Evans Picture OR Library/Alamy DISTRIBUTION Images. Inset courtesy of National Library of Medicine. NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 17 03/04/17 9:16 am 18 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORspecifi SALE c germ OR fromDISTRIBUTION a diseased individual and demon-NOT tookFOR several SALE spores OR DISTRIBUTION on a sliver of wood and injected strate the isolated germ caused that same disease. them into healthy mice. The signs of anthrax soon appeared, and when Koch autopsied the animals, he found their blood swarming with the same type Robert Koch Formalizes Standards to of bacterial cells. Here was the fi rst evidence that a Equate Germs with© InfectiousJones & Bartlett Disease Learning, LLCspecifi c germ was the causative© Jones agent & Bartlett of a specifi Learning, c LLC Robert Koch (FIGURE NOT 1.7 AFOR ) was SALEa German OR countryDISTRIBUTION disease. NOT FOR SALE OR DISTRIBUTION doctor who was well aware of anthrax, a deadly dis- Koch found that growing bacterial cells was not ease that periodically ravaged cattle and sheep and very convenient. Then, in 1880, he observed a slice of also could cause disease in humans. Was anthrax potato on which small masses of bacterial cells, which he termed colonies, were multiplying in number. Koch caused© Jonesby a germ? & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC In 1875, Koch injected mice with the blood from tried adding gelatin to his broth to prepare a similar sheepNOT suffering FOR anthrax.SALE OR He noticedDISTRIBUTION the mice soon solid cultureNOT surface. FOR SALEHe then OR inoculated DISTRIBUTION bacterial developed the same disease signs seen in the sheep. cells on the surface and set the dish aside to incubate. Next, he isolated a few rod-shaped bacterial cells Within 24 hours, visible colonies were growing on from the blood and, with his microscope, watched for the surface, each colony representing a pure culture © Jones &hours Bartlett as the Learning, bacterial cells LLC multiplied, formed tan-© Jonescontaining & Bartlett only one Learning, bacterial LLCtype. By 1884, a poly- NOT FORgled SALE threads, OR andDISTRIBUTION fi nally reverted to spores. He thenNOT saccharideFOR SALE called OR agar DISTRIBUTION that was derived from marine

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Anthrax bacilli NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONSpore Postulate 2 The microorganisms are isolated from the tissues of a dead animal, and a pure culture is prepared. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Postulate 4 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONThe identical microorganisms are isolated and recultivated from the tissue specimens of the experimental animal. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Postulate 3 Microorganisms from the pure culture are inoculated into a healthy, susceptible animal. The disease is © Jones & Bartlett Learning, LLCreproduced. © Jones & Bartlett Learning, LLC (B) (A) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION FIGURE 1.7 A Demonstration of Koch’s Postulates. Robert Koch (A) developed what became known as Koch’s postulates (B) that were used to relate a single microorganism to a single disease. The inset (in the upper right) is a photo of the rod- shaped anthrax bacterial cells. Many rods are swollen with spores (white ovals). »» What is the relationship between postulate © Jones2 and & postulateBartlett 4? Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR(A) Courtesy SALE of National OR Library ofDISTRIBUTION Medicine. (B) Inset courtesy of the CDC. NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 18 03/04/17 9:16 am KEY CONCEPT 1.3 The Classical Golden Age of Microbiology Reveals the Germ 19

Jams, Jellies, and Microorganisms © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC One of the major developmentsNOT FOR in SALE microbiology OR DISTRIBUTION was Robert Koch’s use of a NOT FOR SALE OR DISTRIBUTION solid culture surface on which bacterial colonies would grow. He accomplished this by solidifying beef broth with gelatin. When inoculated onto the surface of the nutritious medium, bacterial cells grew vigorously at room temperature and produced discrete, visible colonies. On occasion, © Jones & however, Bartlett Koch Learning, was dismayed LLC to fi nd that the gelatin © Jonesturned & Bartlett Learning, LLC to liquid because some bacterial species produced a chemical substance that NOT digested FOR the SALE gelatin. OR Moreover, DISTRIBUTION gelatin liquefi ed at the warm NOTincubator FOR SALE OR DISTRIBUTION temperatures commonly used to cultivate many bacterial species. An associate of Koch’s, Walther Hesse, mentioned the problem to his wife and laboratory assistant, Fanny Hesse. She had a possible solution. For years, she had been using a seaweed-derived powder called agar (pronounced ah’gar) to © Jones & solidifyBartlett her jamsLearning, and jellies. LLC Agar was valuable because it ©mixed Jones easily &with Bartlett most Learning, LLC NOT FOR SALEliquids and OR once DISTRIBUTION gelled, it did not liquefy, even at warm incubatorNOT FOR temperatures. SALE OR DISTRIBUTION In 1880, Walther Hesse recommend agar to Koch. Soon Koch was using it routinely to grow bacterial species, and, in 1884, he fi rst mentioned agar in his paper on the isolation of the bacterial organism responsible for tuberculosis. It is noteworthy that Fanny Hesse is one of the fi rst Americans (she was originally from New Jersey) to make a signifi cant contribution to microbiology. © Jones & Bartlett Learning, LLC Fanny Hesse.© Jones & Bartlett Learning, LLC Another key development, the common petri dish (plate), also was invented about this time (1887)NOT by Julius FOR Petri, SALE one of OR Koch’s DISTRIBUTION former assistants. Courtesy of NationalNOT Library ofFOR Medicine. SALE OR DISTRIBUTION

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC algaeNOT replaced FOR gelatin SALE as ORKoch’s DISTRIBUTION preferred solidifying for tuberculosisNOT FOR and SALEcholera. OR In DISTRIBUTION addition, many agent, as MICROFOCUS 1. 3 recounts. other individuals quickly discovered other germs When Koch presented his work, scientists were causing other human diseases ( TABLE 1.1 ). Pas- astonished. Here was the verifi cation of the germ teur’s lab, on the other hand, was more concerned theory that had eluded Pasteur. Koch’s procedures with preventing disease through vaccination. This © Jones &became Bartlett known Learning, as Koch’s LLC postulates and were© Jonesculminated & Bartlett in 1885, Learning, when Pasteur’s LLC rabies vaccine NOT FORquickly SALE adoptedOR DISTRIBUTION as the formalized standards forNOT savedFOR theSALE life ORof a DISTRIBUTIONyoung boy who had been bitten implicating a specifi c germ with a specifi c disease. by a rabid dog. By the turn of the century, the germ FIGURE 1.7 B outlines the four-step process. theory set a new course for studying and treating By applying Koch’s postulates, germ identifi ca- infectious disease. The detailed studies carried out tion in the laboratory became the normal method of by Pasteur and Koch made the discipline of bacte- work. Koch’s lab focused© Jones on disease & Bartlett causation Learning, ( eti- LLCriology, the study of bacterial© Jones organisms, & Bartlett a well- Learning, LLC ology), including theNOT bacterial FOR agentsSALE responsibleOR DISTRIBUTION respected fi eld of study. NOT FOR SALE OR DISTRIBUTION

Concept© Jones and & ReasoningBartlett Learning, Checks 1.3LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION a. How did Pasteur’s studies of wine fermentation and souring suggest to him that germs might cause human infectious disease? b. Assess Lister’s antisepsis procedures and Pasteur’s studies of pébrine to supporting the germ theory. c. Explain why Koch’s postulates were critical to validating the germ theory. © Jones & d.Bartlett How did Learning, the development LLC of pure cultures advance the© Jonesgerm theory? & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 19 03/04/17 9:16 am 20 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION taBle 1.1 Other International Scientists Who Identiﬁ ed Speciﬁ c Human Pathogens During the Classical Golden Age of Microbiology

Investigator (Year)© Jones & Bartlett Learning, Country LLC Disease© (Pathogenic Jones & BartlettAgent) Learning, LLC Otto Obermeier (1868)NOT FOR SALE OR GermanyDISTRIBUTION RelapsingNOT fever FOR (bacterium) SALE OR DISTRIBUTION

Gerhard Hansen (1873) Norway Leprosy (bacterium)

Albert Neisser (1879) Germany Gonorrhea (bacterium) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Charles Laveran (1880) France Malaria (protozoan) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Karl Eberth (1880) Germany Typhoid fever (bacterium)

Edwin Klebs (1883) Germany Diphtheria (bacterium)

© Jones & Bartlett Arthur Nicolaier Learning, (1884) LLC Germany© Jones & Bartlett Learning, Tetanus (bacterium) LLC NOT FOR SALE Theodore Escherich (1885) OR DISTRIBUTION GermanyNOT FOR SALE OR InfantDISTRIBUTION diarrhea (bacterium)

Albert Fraenkel (1886) Germany Pneumonia (bacterium)

David Bruce (1887) Australia Undulant fever (bacterium) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Anton WeichselbaumNOT (1887) FOR SALE OR AustriaDISTRIBUTION CerebrospinalNOT meningitisFOR SALE OR DISTRIBUTION (bacterium)

A. A. Gärtner (1888) Germany Food poisoning/salmonellosis (bacterium)

William© Jones Welch & and Bartlett George Learning, LLC United States © Jones Gas & gangrene Bartlett (bacterium) Learning, LLC NuttallNOT (1892) FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION S. Kitasato and A. Yersin (1894) Japan and France (Independently) Bubonic plague (bacterium)

Emile van Ermengem (1896) Belgium Botulism (bacterium) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE Kiyoshi OR Shiga DISTRIBUTION (1898) Japan NOT FOR SALE OR BacterialDISTRIBUTION dysentery (bacterium) Walter Reed (1900) United States Yellow fever (virus)

Robert Forde and Joseph Everett Great Britain African sleeping sickness Dutton (1902) (protozoan) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Fritz Schaudinn andNOT Erich FOR SALE OR GermanyDISTRIBUTION Syphilis NOT (bacterium) FOR SALE OR DISTRIBUTION Hoffman (1903)

Jules Bordet and Octave France Whooping cough/pertussis Gengou (1906) (bacterium) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC George McCoy and Charles United States Tularemia (bacterium) ChapinNOT (1911)FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 20 03/04/17 9:16 am KEY CONCEPT 1.4 With the Discovery of Other Microbes, the Microbial World Expands 21

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE KeY OR ConCept DISTRIBUTION 1.4 With the DiscoveryNOT ofFOR Other SALE Microbes, OR DISTRIBUTION the Microbial World Expands

Although bacterial organisms© Jones were & Bartlett being discovered Learning, LLCfi rst seen by Leeuwenhoek)© Jones was & another Bartlett major Learning, LLC milestone in understanding infectious disease. In as the agents of someNOT human FOR diseases, SALE why OR couldn’t DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Koch’s postulate confi rm a bacterial origin for dis- fact, Pasteur’s “corpuscular parasites” of pébrine eases such as measles, mumps, smallpox, and yellow were protozoa. Other advances in the study of these fever? Moreover, what were the bacterial organisms types of microbes were dependent on studies in being discovered in the soil doing? tropical medicine. Major advances in understand- © Jones & Bartlett Learning, LLC ing these ©microbes Jones included& Bartlett Charles Learning, Laveran’s LLC dis- OtherNOT Global FOR Pioneers SALE OR Contribute DISTRIBUTION to the New covery (1880)NOT that FOR the SALE protozoan OR DISTRIBUTIONparasite causing Discipline of Microbiology malaria could be found in human blood and David Bruce’s studies (1887) that another protozoan par- In the 1890s, a Russian scientist, Dimitri Ivanowsky, asite was the agent of human sleeping sickness. and Martinus Beijerinck, a Dutch investigator, With these studies, the fi eld of protozoology was independently were studying tobacco mosaic dis- © Jones & Bartlett Learning, LLC © Jonesborn &(FIGURE Bartlett 1.8 Learning, ). LLC ease, which produces mottled and stunted tobacco NOT FOR SALE OR DISTRIBUTION NOT FOR As SALEyou should OR DISTRIBUTION now know, not all microbes leaves. Each independently prepared a homoge- are pathogens; in fact, as described in the chap- nized liquid from diseased plants in the hopes of ter opener, relatively few cause infectious disease. trapping the infectious agent on the fi lter. In fact, Consequently, during the fi rst Golden Age of micro- they discovered that when the liquid that passed biology, other scientists and microbiologists were through a fi lter was applied to healthy tobacco © Jones & Bartlett Learning, LLCkeenly interested in microbes© Jones naturally & Bartlett found in Learning,the LLC plants, the leaves became mottled and stunted. NOT FOR SALE OR DISTRIBUTIONsoil, and they wanted to NOTunderstand FOR SALEthe ecological OR DISTRIBUTION Ivanowsky simply assumed bacterial cells somehow importance of these nonpathogenic microbes. The had slipped through the fi lter, whereas Beijerinck Russian soil scientist Sergei Winogradsky, a stu- suggested that the liquid was a “contagious, liv- dent of de Bary’s, and Martinus Beijerinck discov- ing liquid” that acted like a poison or virus (virus = ered that some bacterial organisms could convert “poison”).© Jones Then, & Bartlettin 1898, theLearning, causative LLC agent for © Jones & Bartlett Learning, LLC inert atmospheric nitrogen gas (N ) into biolog- animalNOT hoof-and-mouth FOR SALE OR disease DISTRIBUTION was found to be NOT FOR SALE OR DISTRIBUTION2 ically useable ammonia (NH ) that plants need. another fi lterable liquid, and, in 1901, American 3 Winogradsky and Beijerinck each developed many Walter Reed, a United States Army physician, con- of the laboratory methods essential to the study of cluded that the agent responsible for yellow fever soil microbes, while uncovering the essential roles in humans also was a virus. With these discoveries, such microorganisms play in the recycling of mat- © Jones &the Bartlett discipline Learning, of virology LLC , the study of viruses, was© Jones & Bartlett Learning, LLC ter on a global scale. As the founders of microbial NOT FORlaunched. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ecology , Winogradsky and Beijerinck laid the foun- While scientists like Pasteur and Koch were dation for what we know today about many of the investigating the bacterial contribution to the so-called microbial workforce mentioned in the infectious disease process, others were identifying chapter opener. other types of disease-causing microbes. Fungi were © Jones & Bartlett Learning, LLC Today, many microbiologists© Jones are & still Bartlett searching Learning, LLC found to cause plant diseases and such diseases for, fi nding, and trying to understand the roles of were studied extensivelyNOT byFOR Anton SALE de BaryOR DISTRIBUTIONin the NOT FOR SALE OR DISTRIBUTION microorganisms in the environment as well as in 1860s. As already mentioned in this chapter, Pas- health and disease. In fact, less than 2% of all micro- teur identifi ed the role of fungal yeasts (fi rst seen by organisms on Earth have been identifi ed and many Leeuwenhoek) with fermentation. Importantly, the fewer cultured, so there is still a lot to be discovered recognition that some fungi were linked to human © Jones & Bartlett Learning, LLC and studied© Jonesin the microbial & Bartlett world! Learning, LLC skin NOTdiseases FOR was SALE proposed OR DISTRIBUTIONas early as 1841 when NOT FOR SALE OR DISTRIBUTION a Hungarian physician, David Gruby, discovered a fungus associated with human scalp infections. The Microbial World Can Be Cataloged into These discoveries led to the development of the Unique Groups fi eld of mycology , the study of fungi. As time went on, more and more microbes were © Jones & BartlettThe realization Learning, that infectiousLLC diseases could be© Jonesidentifi & edBartlett and studied. Learning, Let’s briefl LLC y survey what we NOT FORcaused SALE by OR protozoa DISTRIBUTION (again part of the animalculesNOT knowFOR aboutSALE these OR majorDISTRIBUTION groups of microorganisms.

9781284101041_CH01_001_034.indd 21 03/04/17 9:16 am 22 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

studies

in the including disciplines of © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Bacteriology Mycology Parasitology Virology Virus-like Agents (multicellular)

Phycology Protozoology © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR FIGURE SALE 1. OR8 Microbiology DISTRIBUTION Disciplines. This simple conceptNOT map showsFOR the SALE relationship OR DISTRIBUTION between microbiology and its various disciplines. Phycology is the study of algae and parasitology is the study of animal parasites, which traditionally includes the parasitic protozoa and the animal parasites (worms).

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Bacteria and ArchaeaNOT FOR SALE OR DISTRIBUTIONsprings), extremely salty NOT(such FORas the SALE Dead Sea), OR orDISTRIBUTION of extremely low pH (such as acid mine drainage). It is estimated that there might be more than These so-called extremophiles evolved many adap- 10 million bacterial species. Most are very small, tations to survive in these extreme environments. single-celled (unicellular) organisms, although © Jones & Bartlett Learning, LLC Conversely,© Jonesmany other & Bartlett archaeal Learning, organisms LLC nor- some form fi laments, and the majority associate in mally grow in temperate soils and water and are an a bacterialNOT FOR community SALE OR called DISTRIBUTION a “biofi lm.” Almost integral partNOT of FORthe microbiome SALE OR in DISTRIBUTION animal digestive all bacterial cells have a rigid cell wall and many tracts. No archaeal members are known to be patho- common ones are spherical, spiral, or rod-shaped gens, but like the bacterial microbes, they are an (FIGURE 1.9 A ). They lack a cell nucleus and most of important part of Earth’s microbial workforce. the typical membrane-enclosed cellular compart- © Jones &ments Bartlett typical Learning, of other microbesLLC and multicellular© Jones & Bartlett Learning, LLC NOT FORorganisms. SALE OR Many DISTRIBUTION bacterial organisms get their foodNOT VirusesFOR SALE OR DISTRIBUTION from the environment, although some make their Although not correctly labeled as microorganisms, own food through photosynthesis ( FIGURE 1.9 B ). these “infectious agents” currently consist of more Bacterial cells are found in most all environments, than 100 million known types. Probably, most every making up, as previously© Jones mentioned, & Bartlett a large Learning, per- LLCcell on Earth can be infected© Jones by some & typeBartlett of virus. Learning, LLC centage of the Earth’s microbial workforce. Viruses are not cellular and cannot be grown in cul- In addition to theNOT disease-causing FOR SALE members, OR DISTRIBUTION some ture. They have a core of nucleicNOT FOR acid (DNASALE or OR RNA) DISTRIBUTION are responsible for food spoilage, whereas others are surrounded by a protein coat. Among the features useful in the food industry. Many bacterial members, used to identify viruses are morphology (shape), along with several fungi, are decomposers , organisms genetic material (DNA, RNA), and biological prop- that ©recycle Jones nutrients & Bartlett from dead Learning, organisms. LLC erties (the© organism, Jones & tissue, Bartlett or cell Learning, type infected). LLC BasedNOT onFOR recent SALE biochemical OR DISTRIBUTION and molecular stud- VirusesNOT infect FOR organisms SALE ORfor DISTRIBUTIONone reason only: ies, many bacterial organisms have been reassigned to replicate. Viruses in the air or water, for example, into another unique evolutionary group, called the cannot replicate because they need the metabolic Archaea. Although they look like bacterial cells machinery and chemical building blocks found inside when observed with the microscope, many of the living cells. Of the known viruses, only a small per- © Jones &fi rst Bartlett members Learning, to be identifi LLC ed grew in environments© Jonescentage & Bartlett cause disease Learning, in humans. LLC Polio, the fl u, mea- NOT FORthat SALE are extremelyOR DISTRIBUTION hot (such as the Yellowstone hotNOT sles,FOR AIDS, SALE and OR smallpox DISTRIBUTION are examples (FIGURE 1.9 C ).

9781284101041_CH01_001_034.indd 22 03/04/17 9:16 am KEY CONCEPT 1.4 With the Discovery of Other Microbes, the Microbial World Expands 23

©(C) Jones & Bartlett Learning, LLC (D) © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

(E) (F)

FIGURE© Jones 1.9 Groups & Bartlett of Microorganisms. Learning, (A) A LLC light microscope image of rod-shaped© Jones cells & of Bartlett Bacillus cereus Learning, (stained purple), LLC a normal inhabitant of the soil. (Bar = 10 μm.) (B) A light microscope image of fi lamentous strands of Anabaena , a photosynthetic bacterium. (Bar = 100 μm.) NOT FOR SALE(C) OR False-color electron microscope image of smallpox viruses. (Bar = 500 nm.) DISTRIBUTION NOT FOR SALE OR(D) DISTRIBUTION A typical blue-gray Penicillium mold growing on a loaf of bread. (E) A light microscope image of the colonial green alga Volvox. (Bar = 300 μm.) (F) A light microscope image of the ribbon-like cells of the protist Trypanosoma , the causative agent of African sleeping sickness. (Bar = 10 μm.) »» Within these groups, why don’t organisms like Anabaena and Volvox cause disease? © Jones &(A, B, Bartlett E, F) Courtesy of Dr. Learning, Jeffrey Pommerville. (C) LLC © Image Source Trading Ltd/Shutterstock. (D) © Jones© &Jones Bartlett Learning. & Photographed Bartlett by Kimberly Learning, Potvin. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 23 03/04/17 9:16 am 24 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE The other OR DISTRIBUTIONgroups of microbes have a cell nucleusNOT impartFOR SALE distinctive OR DISTRIBUTIONﬂ avors in foods such as cheeses. and a variety of internal, membrane-bound cellular Together with many bacterial species, numerous compartments. molds play a major role as decomposers.

Fungi Protists © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC The fungi include the unicellular yeasts and the The protists consist mostly of protozoa and single- multicellular mushroomsNOT andFOR molds SALE (FIGURE OR DISTRIBUTION 1.9 D ). celled algae. Some are freeNOT living, FOR whereas SALE ORothers DISTRIBUTION About 100,000 species of fungi have been described; live in association with plants or animals. Move- however, there might be as many as 1.5 million spe- ment, if present, is achieved by fl agella or cilia or by cies in nature. a crawling motion. Other© Jones than & some Bartlett yeasts, Learning, molds grow LLC as fi la- Protists© Jonesobtain &nutrients Bartlett inLearning, different LLCways. mentsNOT with FOR rigid cellSALE walls. OR Most DISTRIBUTION grow best in warm, Some absorbNOT nutrients FOR SALE from theOR surrounding DISTRIBUTION envi- moist places and secrete digestive enzymes that ronment or ingest smaller microorganisms. The break down nutrients into smaller bits that can be unicellular, colonial, and fi lamentous algae have absorbed easily across the cell wall. Fungi, there- a rigid cell wall and can carry out photosynthesis fore, live in their own food supply. If that source of (FIGURE 1.9 E). The aquatic protists also provide © Jones &food Bartlett is a human, Learning, diseases LLC such as ringworm or vagi-© Jonesenergy & andBartlett organic Learning, compounds LLC for the lower trophic NOT FORnal SALE yeast ORinfections DISTRIBUTION can result. NOT levelsFOR ofSALE the food OR web. DISTRIBUTION Some protists (the protozoa) For the pharmaceutical industry, some fungi are capable of causing diseases in animals, includ- are sources for useful products, such as antibiot- ing humans; these include malaria, several types of ics. Others molds are used in the food industry to diarrhea, and sleeping sickness (FIGURE 1.9 F ). © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Concept and ReasoningNOT FOR Checks SALE 1.4 OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

a. Describe how viruses were discovered as disease-causing agents. b. What signifi cant discoveries added the fungi and protozoa to the growing list of microbes? c. Judge the signifi cance of the pioneering studies carried out by Winogradsky and Beijerinck. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Chapter Challenge B

By the end of the fi rst Golden Age of microbiology (1915), all the major groups of microbes had been identifi ed. © Jones & Bartlett Learning, QUESTION B:LLC Construct a diagram or table that© Jones reveals how & Bartlettyou could tell Learning, bacteria, viruses, LLC fungi, protozoa, and NOT FOR SALE OR DISTRIBUTIONalgae apart from one another using structuralNOT and/or FOR functional SALE characteristics. OR DISTRIBUTION You can fi nd answers online in Appendix F .

KeY ConCept 1.5 The Second Golden Age of Microbiology Involves the Birth © Jones &of Bartlett Molecular Learning, Biology LLC and Chemotherapy© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The 1940s brought the birth of molecular genet- model systems with which to explore the molecular ics and the development of one of the greatest workings of life and to discover general principles in breakthroughs© Jones &that Bartlett would revolutionizeLearning, LLC medicine’s biology. Consequently,© Jones & Bartlett beginning Learning, around 1940, LLC the ability to treat and eliminate infectious disease— second Golden Age of microbiology emerged. antibiotics.NOT FOR SALE OR DISTRIBUTION Here areNOT a few FOR of theSALE scientists OR DISTRIBUTION who used microbial model systems and viruses: Molecular Biology Often Relies on ▶ George Beadle and Edward Tatum (1941) Microorganisms as Model Systems used the fungus Neurospora to demon- © Jones &Being Bartlett small, Learning, easy to grow, LLC and having fast repro-© Jones & Bartlettstrate that Learning, genes direct LLC the synthesis of NOT FORductive SALE rates, OR DISTRIBUTIONmicrobes are perfect research tools orNOT FOR SALEproteins. OR DISTRIBUTION

9781284101041_CH01_001_034.indd 24 03/04/17 9:16 am KEY CONCEPT 1.5 The Second Golden Age of Microbiology Involves the Birth of Molecular 25

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE▶ Salvador OR DISTRIBUTION Luria and Max Delbrück (1943)NOT forFOR the SALE fi rst time OR bacterial DISTRIBUTION cells were seen as being used the bacterium Escherichia coli to show cellular like all other microbes, plants, and animals. that mutations could occur spontaneously. However, studies showed that they were organized ▶ Oswald Avery, Colin MacLeod, and Maclyn in a structurally different way from other organisms. McCarty (1944) used the bacterium Strep- It was known that animal and plant cells con- tococcus pneumoniae© Jones to & suggest Bartlett that Learning, DNA is LLCtained a cell nucleus ©that Jones houses & Bartlettthe genetic Learning, LLC the genetic materialNOT FOR in all SALE cells. OR DISTRIBUTIONinstructions in the form NOTof chromosomes FOR SALE and OR that DISTRIBUTION ▶ Alfred Hershey and Martha Chase (1952) the nucleus was separated physically from other cell used a virus that infects bacterial cells to structures by a membrane envelope ( FIGURE 1.10 A ). confi rm that DNA is the genetic material. This type of cellular organization is called eukary- ▶ © Jones Francis &Crick Bartlett (1958) Learning, used E. coli LLCand a virus otic (eu =© “true”; Jones karyon & Bartlett = “nucleus”). Learning, Microscope LLC to show how the DNA genetic code works to observations of the protists and fungi had revealed NOTmake FOR individual SALE proteins.OR DISTRIBUTION that theseNOT organisms FOR SALEalso have OR a DISTRIBUTIONeukaryotic organization. Thus, not only are all plants and animals Again, microbes were at the forefront in answer- eukaryotes , so are the microorganisms that coming fundamental questions that applied to all of prise the fungi and protists. biology. In addition, during this second Golden Age, Electron microscope studies revealed that bacte- © Jones &other Bartlett studies Learning, illuminated LLC the basic structural orga-© Jones & Bartlett Learning, LLC rial (and archaeal) cells had few of the internal com- NOT FORnization SALE ofOR microbes. DISTRIBUTION NOT FOR SALE OR DISTRIBUTION partments typical of eukaryotic cells. They lacked a cell nucleus, indicating the DNA was not sur- Two Types of Cellular Organization rounded by a membrane envelope ( FIGURE 1.10 B ). Are Realized Therefore, members of the Bacteria and Archaea The small size of bacterial© Jones cells & Bartlett hindered Learning, scien- LLChave a prokaryotic (pro =© “before”) Jones &type Bartlett of cellular Learning, LLC tists’ abilities to confiNOT rm ifFOR these SALE cells were OR DISTRIBUTIONsimilar organization and representNOT prokaryotesFOR SALE. Impor-OR DISTRIBUTION to other cellular organisms in organization or if tantly, there also are many genetic and molecular the cells were just “bags of enzymes.” In the 1940s differences between bacterial and archaeal cells, and 1950s, a new type of microscope—the electron accounting for their split into separate and unique microscope—was developed that could magnify microbial groups. Incidentally, because viruses lack objects© Jonesand cells & thousands Bartlett ofLearning, times better LLC than typ- a cellular ©organization, Jones & Bartlett they are neitherLearning, prokaryotes LLC ical lightNOT microscopes. FOR SALE With OR the DISTRIBUTION electron microscope, nor eukaryotes.NOT FOR SALE OR DISTRIBUTION

FIGURE 1.1 0 False-Color Images of Eukaryotic and Prokaryotic Cells. (A) A false-color electron microscope image of a protist cell. All eukaryotes, including the protists and fungi, have their DNA enclosed in a cell nucleus. (Bar = 3 μm.) (B) A false- color electron microscope image of bacterial cells. (Bar = 0.5 μm.) »» How is the DNA in the eukaryotic cell structurally different © Jones &from Bartlett the DNA inLearning, the bacterial cell?LLC © Jones & Bartlett Learning, LLC NOT FOR(A) SALE © London School OR of Hygiene DISTRIBUTION & Tropical Medicine/Science Source. (B) © A. DOWSETT, PUBLIC HEALTHNOT ENGLAND/SCIENCE FOR PHOTOSALE LIBRARY OR/Getty Images.DISTRIBUTION

9781284101041_CH01_001_034.indd 25 03/04/17 9:16 am 26 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR Antibiotics SALE OR AreDISTRIBUTION Used to Cure NOT FOR In SALE1928, Alexander OR DISTRIBUTION Fleming, a Scottish scientist, Infectious Disease discovered a mold growing in one of his bacterial cul- In 1910, another coworker of Koch’s, Paul Ehrlich, tures (FIGURE 1.11 A, B ). The mold, a species of Pen- synthesized the ﬁ rst chemical capable of killing icillium, killed the bacterial colonies that were near pathogens without © severely Jones damaging& Bartlett the Learning, tissue LLCthe mold. He named the© antimicrobialJones & Bartlett substance Learning, LLC penicillin and soon discovered penicillin would kill surrounding the infection.NOT FORThis so-called SALE OR magic DISTRIBUTION bul- NOT FOR SALE OR DISTRIBUTION let, an arsenic-based agent called salvarsan, could other bacterial pathogens, as well. In 1940, research cure syphilis, a serious sexually transmitted infec- headed by biochemists Howard Florey and Ernst tion. With the birth of antibacterial chemotherapy , Chain developed a way to mass produce penicillin, the use of antimicrobial chemicals to kill microbes which would become a godsend in curing bacterial would© Jones become & an Bartlett important Learning, branch LLC of medical infections© during Jones World & Bartlett War II (Learning, FIGURE 1.11 LLC C ). As microbiologyNOT FOR and SALE medicine. OR DISTRIBUTION other antibacterialNOT FOR chemicals SALE OR were DISTRIBUTION discovered, the

FIGURE 1.1 1 Fleming and Penicillin. (A) Artist’s drawing of Fleming in his laboratory. (B) Fleming’s notes and drawing on the inhibition of bacterial growth by the fungus Penicillium. (C) A World War II poster touting the beneﬁ ts of penicillin and illustrat- ing the great enthusiasm in the United States for treating infectious diseases in war casualties. »» In (B), why didn’t penicillin © Jones &kill Bartlettthe bacterial Learning, colonies farther LLC away from the fungus? © Jones & Bartlett Learning, LLC NOT FOR(A) SALE © Science Source. OR (B) ©DISTRIBUTION St. Mary’s Hospital Medical School/Science Source. (C) Used with permissionNOT from Pﬁ zer,FOR Inc. All rightsSALE reserved. OR DISTRIBUTION

9781284101041_CH01_001_034.indd 26 11/04/17 4:57 pm KEY CONCEPT 1.6 A Third Golden Age of Microbiology Is Now 27

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORterm SALE antibiotic OR DISTRIBUTION was coined to refer to those antimi-NOT believedFOR SALE all major OR DISTRIBUTIONbacterial infections would soon crobial substances naturally produced by mold and become rare events due to antibiotic chemotherapy. bacterial species that inhibit growth or kill other What was ignored was the mounting evidence that microorganisms. bacterial species were becoming resistant to or tol- By the 1950s, penicillin and several other anti- erant of antibiotics. Still, antibiotics represent one biotics were established© Jones treatments & Bartlett in medical Learning, prac- LLCof the greatest breakthroughs© Jones in medicine & Bartlett and they Learning, LLC tice. In fact, by the mid-1960s,NOT FOR many SALE health OR expertsDISTRIBUTION have saved millions of livesNOT since FOR their SALE introduction. OR DISTRIBUTION

Concept and Reasoning Checks 1.5 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC a. What roles did microorganisms (and viruses) play in understanding general principles of molecular biology? b. NOT Distinguish FOR between SALE prokaryoticOR DISTRIBUTION and eukaryotic cells. NOT FOR SALE OR DISTRIBUTION c. Assess the importance of Fleming’s discovery and Florey and Chain’s production of penicillin.

A Third Golden Age of Microbiology Is Now © Jones & Bartlett KeY ConCept Learning, LLC 1.6 © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Today, microbiology again ﬁ nds itself on the world concern infectious diseases that today are respon- stage, in part from the new age of exploration in sible for 16% of all deaths globally (FIGURE 1.12 ). which unique and diverse microbes are being discovered in abundance around© Jones the world,& Bartlett as described Learning, in LLC © Jones & Bartlett Learning, LLC the chapter opener. In addition, biotechnology has Microbiology Continues to Face made use of the naturalNOT and FOR genetically SALE ORengineered DISTRIBUTION Many Challenges NOT FOR SALE OR DISTRIBUTION abilities of microbial agents to carry out biological The resurgence of infectious disease has brought processes for industrial/commercial/medical appli- the subject back into the mainstream of epidemi- cations. In the latest Golden Age, microbiology ology. Even in the United States, more than 100,000 again© is Jones making & important Bartlett contributionsLearning, LLC to the life people die© each Jones year &from Bartlett bacterial Learning, infections, LLC mak- sciencesNOT and FOR humanity. SALE OR DISTRIBUTION ing them NOTthe fourth FOR leading SALE cause OR DISTRIBUTION of death. In fact, However, the third Golden Age of microbiology on a global scale, infectious diseases are spreading also faces several challenges, many of which still geographically faster than at any time in history.

Respiratory infections © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Diarrheal diseases NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION HIV/AIDS

Tuberculosis

Malaria

Measles

Hepatitis B

© Jones & BartlettOther infectiousLearning, diseases LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 0 0.5 11.5 2 2.5 3 3.5 4 4.5 Number of Deaths (millions)

FIGURE 1.1 2 Global Mortality from Infectious Diseases—2015. On a global scale, some 15 million deaths annually are © Jones &caused Bartlett by infectious Learning, diseases. LLC »» Identify some of the “other© infectious Jones diseases.” & Bartlett Learning, LLC NOT FORData SALE from World HealthOR Statistics DISTRIBUTION 2015 : World Health Organization. NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 27 03/04/17 9:16 am 28 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

Disease Transmission Experts estimate that© Jonesmore than & Bartlett 3 billion Learning, people LLC © Jones & Bartlett Learning, LLC (9 million per day) onNOT some FOR 24 million SALE fl ights OR traveled DISTRIBUTION NOT FOR SALE OR DISTRIBUTION by air in 2015, making an outbreak or an epidemic in one part of the world only a few fl ight hours away from becoming a potentially dangerous threat in another region of the globe. It is a sobering thought (A) to realize© Jones that since & Bartlett 2002, the Learning, WHO has verifi LLC ed more © Jones & Bartlett Learning, LLC than NOT 1,100 FOR epidemic SALE events OR worldwide.DISTRIBUTION Unlike past NOT FOR SALE OR DISTRIBUTION generations, today’s highly mobile, interdependent, and interconnected world provides potential oppor- tunities for the rapid spread of infectious diseases.

© Jones & Emerging Bartlett and Learning, Reemerging LLC Infectious Diseases © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Infectious diseases today not only have the potential to spread faster, they also are appearing with greater frequency and intensity. Over the past few decades, new diseases have been identifi ed at the unprecedented rate ©of Jones one or &more Bartlett per year, Learning, such LLC © Jones & Bartlett Learning, LLC that today there areNOT nearly FOR 40 SALEinfectious OR diseases DISTRIBUTION NOT FOR SALE OR DISTRIBUTION present that were unknown a generation ago. These diseases fall into one of two groups. An emerging infectious disease is one that has recently surfaced in the human population for the fi rst ©time. Jones Among & Bartlettthe more Learning, newsworthy LLC have been © Jones & Bartlett Learning, LLC AIDS,NOT severe FOR acute SALE respiratory OR DISTRIBUTION syndrome (SARS), NOT FOR SALE OR DISTRIBUTION Lyme disease, bird fl u, and most recently, Ebola virus disease in West Africa and Zika virus infection in the Western Hemisphere. There is no cure for any (B) of these, and, undoubtedly, there are more disease- FIGURE 1.1 3 Emerging Disease Threats: Natural and © Jones &causing Bartlett pathogens Learning, ready LLC to emerge. © JonesIntentional. & Bartlett (A) West Learning, Nile virus (WNV) LLC is just one of several NOT FOR SALEA reemerging OR DISTRIBUTION infectious disease is one that hasNOT agentsFOR SALEresponsible OR for DISTRIBUTION emerging or reemerging diseases. existed in the past but is now showing resurgence in Methods have been designed that individuals can use to resistant forms and expansion in geographic range. protect themselves from mosquitoes that spread the virus. Among the more prominent reemerging diseases (B) Combating the threat of bioterrorism often requires spe- cial equipment and protection because many agents seen are drug-resistant tuberculosis, cholera, dengue © Jones & Bartlett Learning, LLCas possible bioweapons could© Jonesbe spread & through Bartlett the Learning,air. LLC fever, and, for the fi rst time in the Western Hemi- NOT FOR SALE OR DISTRIBUTION»» How do these suits compareNOT to thoseFOR to SALE protect ORfrom DISTRIBUTION a sphere, West Nile virus disease ( FIGURE 1.13 A ). miasma ( see Figure 1.3)? Therefore, until better surveillance of disease out- (A) Reproduced with permission of the New York State Department of Health. (B) © Photodisc. breaks is established, and more and better vaccines and antimicrobial drugs are developed, emerging and ©reemerging Jones & diseases Bartlett will Learning, remain a challengeLLC to including© habitat Jones destruction,& Bartlett Learning,increased contactLLC publicNOT health FOR and SALE microbiology. OR DISTRIBUTION between humansNOT FOR and SALEwild animals, OR DISTRIBUTION climate change, Epidemiologists and health experts estimate and the trade in global agricultural products further that about 60% of infectious diseases in humans are drive disease transmission. Therefore, scientists in zoonotic diseases , that is, diseases that are spread human, veterinary (domestic and wild), and envi- from wild or domesticated animals to humans. ronmental health are establishing a worldwide col- © Jones &Examples Bartlett includeLearning, AIDS, LLC Ebola virus disease,© Joneslaboration & Bartlett and communication Learning, LLC network called One NOT FORZika SALE virus OR infection, DISTRIBUTION and infl uenza. Other factorsNOT HealthFOR SALE . Rather OR than DISTRIBUTION treat each infectious disease in

9781284101041_CH01_001_034.indd 28 03/04/17 9:16 am KEY CONCEPT 1.6 A Third Golden Age of Microbiology Is Now 29

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORisolation, SALE OR the DISTRIBUTIONstrategy of One Health is to monitorNOT patterns)FOR SALE could OR affect DISTRIBUTION the frequency and distribution and combine all information on human, animal, and of infectious diseases around the world in the coming environmental health in such a way that a potential decades. For example, as temperatures rise in various outbreak of disease can be predicted before it actu- regions of the world, mosquitoes might broaden their ally happens. This challenge is daunting but doable. range and, in so doing, spread diseases like malaria The success of One ©Health Jones is critical & Bartlett to the Learning, control LLCand dengue fever to more temperate© Jones climates,& Bartlett includ- Learning, LLC of infectious diseasesNOT and FORis indispensable SALE OR for DISTRIBUTION helping North America and Europe.NOT Warming FOR SALE ocean ORwaters DISTRIBUTION ing maintain human health. also could provide ideal environments for the spread of waterborne diseases like cholera. Increased Antibiotic Resistance Microbiologists, epidemiologists, climate scien- Another© Jones challenge & Bartlett concerns Learning, our increasing LLC inability tists, and ©many Jones others & Bartlettare studying Learning, new strategies LLC to limit potential disease spread before the caus- to fi ghtNOT infectious FOR SALE disease OR because DISTRIBUTION so many patho- NOT FOR SALE OR DISTRIBUTION gens are now resistant to one or more antibiotics, ative agents have an opportunity to be established. and such antibiotic resistance is developing faster In so doing, researchers need to understand better than new antibiotics are being discovered. Ever since the dynamics of climate change and recognize how it was recognized that pathogens could develop into such changes might affect the behaviors of poten- © Jones &superbugs Bartlett , whichLearning, are microbes LLC that are resistant© Jonestially & emerging Bartlett and Learning, reemerging LLC diseases that could NOT FORto SALE multiple OR antibiotics, DISTRIBUTION a crusade has been wagedNOT affectFOR theSALE health OR of DISTRIBUTION humans, livestock, plants, and to restrain the inappropriate use of these drugs by wildlife. Climate change coupled with the ubiquity doctors and to educate patients not to demand anti- and speed of air travel and the expanding evolution biotics in uncalled-for situations. of antibiotic resistance could work synergistically to The challenge facing microbiologists and the cause major epidemics, or even pandemics, if micro- medical community© is Jones to fi nd & newBartlett and effectiveLearning, LLCbiologists and health authorities© Jones don’t & Bartlett fi nd ways Learning, to LLC antibiotics to whichNOT pathogens FOR SALE will not OR develop DISTRIBUTION constantly survey the microbialNOT FOR landscape SALE andOR toDISTRIBUTION resistance quickly before the current arsenal is use- decrease the burden of infectious disease. less. Unfortunately, the growing threat of antibiotic resistance has been accompanied by a decline Studies in Microbial Ecology and Evolution Also Are Helping to Drive the New Golden Age in new© Jonesdrug discovery & Bartlett and Learning,an increase LLCin the time © Jones & Bartlett Learning, LLC to develop a drug from discovery to market. Conse- NOT FOR SALE OR DISTRIBUTION Since the timeNOT of FOR the fi rstSALE Golden OR Age DISTRIBUTION of microbiology, quently, antibiotic resistance has become a major microbiologists have wanted to know how a microbe health threat and one of the most important chal- interacts, survives, and thrives in the environment. lenges facing microbiology today. Today, microbiology is less concerned with a specifi c microbe and more concerned with the relationships © Jones & Bioterrorism Bartlett Learning, LLC © Jonesamong & microorganismsBartlett Learning, and with LLC their environment. NOT FOR The SALE intentional OR DISTRIBUTION or threatened use of biologicalNOT FOR SALE OR DISTRIBUTION agents to cause fear in or actually infl ict death or dis- Microbial Ecology ease upon a large population is referred to as bioter- Microbial ecology, which was started by Winogradsky rorism . Most of the recognized biological agents for and Beijerinck, involves the study of microbial bioterrorism are microorganisms, viruses, or micro- © Jones & Bartlett Learning, LLCdynamics in the environment© Jones and their & Bartlett interactions Learning, LLC bial toxins that are bringing diseases like anthrax, with each other and with other organisms. Tradi- smallpox, and plagueNOT back FOR into SALEthe human OR DISTRIBUTIONpsyche tional methods of microbialNOT ecology FOR required SALE organ-OR DISTRIBUTION (FIGURE 1.13 B). To minimize the use of these agents isms from an environment be isolated and cultivated to infl ict mass casualties, the challenge to the scien- in the laboratory so that they can be characterized tifi c community and microbiologists is to improve and identifi ed. Unfortunately, up to 98% of micro- the ways that bioterror agents are detected, dis- © Jones & Bartlett Learning, LLC organisms© do Jones not grow & Bartlett in a laboratory Learning, culture LLC and, cover effective measures to protect the public, and NOT FOR SALE OR DISTRIBUTION therefore,NOT they FORcannot SALE be studied OR DISTRIBUTION visually. In spite develop new and effective treatments against these of this, today many microbiologists, armed with pathogens for individuals or whole populations. genetic, molecular, and biotechnology tools, can study and characterize these uncultured microbes. Climate Change and Infectious Disease Today researchers are discovering that most © Jones & A Bartlettvery controversial Learning, issue LLC is how climate change© Jonesmicrobes & Bartlett do not actLearning, as individual LLC entities; rather, in NOT FOR(including SALE OR warming DISTRIBUTION temperatures and altering rainfallNOT natureFOR SALEthey survive OR DISTRIBUTION in complex communities called

9781284101041_CH01_001_034.indd 29 03/04/17 9:16 am 30 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT MicrobialFOR SALE Evolution OR DISTRIBUTION It was Charles Darwin—another of the scientists who combined observation with a “prepared mind”—who in 1859 fi rst outlined the principles of evolution. © Jones & Bartlett Learning, LLCToday, evolutionary theory© Jonesis the unifying & Bartlett force Learning, in LLC NOT FOR SALE OR DISTRIBUTIONmodern biology, tying togetherNOT suchFOR distinct SALE fi ORelds asDISTRIBUTION genetics, ecology, medicine, and, yes, microbiology. Like all life, microorganisms evolve. In fact, microbial evolution was occurring for some 2 billion years before the fi rst truly eukaryotic cells appeared © Jones & Bartlett Learning, LLC on the planet.© Jones Although & Bartlett challenging Learning, to study, LLC it is NOT FOR SALE OR DISTRIBUTION possible todayNOT toFOR “replay SALE history” OR DISTRIBUTION by following the accumulation of unpredictable, chance events that lead to evolutionary novelty, which is a hallmark of the microbes. In addition, microbial evolution studies are putting together new approaches to improve © Jones & Bartlett Learning, LLC © Jonesagricultural & Bartlett productivity, Learning, to monitor LLC and assess cli- NOT FOR FIGURE SALE 1.OR1 4 DISTRIBUTION A Biofi lm. Plaque (the false-colored pinkNOT mateFOR change,SALE ORand DISTRIBUTIONeven to produce clean fuels and crust) typically found on tooth surfaces is an example of a energy. The new fi eld of evolutionary medicine is biofi lm. Left untreated, it might result in tooth decay. »» How providing new strategies to slow the evolution of do these examples of microbes fi t into the concept of the global antibiotic resistance, to treat infectious diseases, and microbial workforce? © Jones & Bartlett Learning, LLCto better understand the ©role Jones of microbes & Bartlett in human Learning, LLC © STEVE GSCHMEISSNER/Science Photo Library/Getty. NOT FOR SALE OR DISTRIBUTIONhealth. One has to wonderNOT what FOR Darwin SALE would OR make DISTRIBUTION of the microbial world if he were alive today. biofi lms . For example, the whitish, gooey plaque In conclusion , microbiology (from then until on your teeth is an example of a bacterial biofi lm now) has gone from observing the fi rst microbes as (FIGURE 1.14 ). Microbes in biofi lms act very differently curiosities (Leeuwenhoek) to identifying and study- than ©individual Jones &cells, Bartlett and the Learning, biofi lms can LLC be diffi cult ing individual© Jones microorganisms & Bartlett asLearning, pathogens LLC (Pas- to treatNOT when FOR they SALE cause chronicOR DISTRIBUTION infectious disease. teur, Koch,NOT and others)FOR SALE to appreciating OR DISTRIBUTION microbiomes The discovered versatility of many bacterial as the engines that support all life on Earth (today). and archaeal species is being applied to problems Yet, over this span of 300-plus years, microbiolo- that have the potential to benefi t the planet. As the gists have only discovered perhaps 2% of all micro- highly respected naturalist, E. O. Wilson has stated, bial species. Microbiology from then until now has © Jones &“ If Bartlett I could do Learning, it all over again, LLC and relive my vision in© Jonescome & a Bartlettlong way Learning,but has a much LLC longer way yet to NOT FORthe SALE 21st century, OR DISTRIBUTION I would be a microbial ecologist. ” NOT goFOR and SALE many challengesOR DISTRIBUTION to face.

Concept and Reasoning Checks 1.6 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC a. Briefl y, discuss four examples of the challenges facing microbiology today. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

© Jones Chapter& Bartlett Challenge Learning, C LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Many of the microbes that fi rst occupied the minds and work of the early microbial pioneers like Pasteur and Koch still challenge microbiologists today. QUESTION C: Describe the natural and intentional disease threats challenging microbiology today, explaining why they are still so prominent even with all the advances in medical science and microbiology. © Jones & You can fi nd answers online in Bartlett Learning, LLCAppendix F . © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 30 03/04/17 9:16 am Chapter Self-Test 31

Concept 1.1 The Discovery© Jones of Microbes& Bartlett Leads Learning, to LLC Concept 1.4 With the Discovery© Jones of Other& Bartlett Microbes, Learning, LLC Questioning Their OriginsNOT FOR SALE OR DISTRIBUTIONthe Microbial World ExpandsNOT FOR SALE OR DISTRIBUTION 1. The observations with the microscope made by 9. Ivanowsky and Beijerinck provided the fi rst evidence Hooke and especially Leeuwenhoek, who reported for viruses as infectious agents. the existence of animalcules (microorganisms), 10. Winogradsky and Beijerinck recognized the benefi cial sparked interest in an unknown world of microscopic roles played by microorganisms found in the environ- ©life. Jones ( Figure & 1.2 Bartlett) Learning, LLC ment.© Jones & Bartlett Learning, LLC 2. The controversy over spontaneous generation initi- 11. Microbes include the Bacteria and Archaea, viruses, NOTated the need for accurate scientifi c experimentation, FOR SALE OR DISTRIBUTION fungi,NOT and protists FOR SALE(algae and OR protozoa). DISTRIBUTION (Figure 1.9) which then provided the means to refute the concept. Concept 1.5 A Second Golden Age of Microbiology Concept 1.2 Disease Transmission Involves the Birth of Molecular Biology and Can Be Prevented Chemotherapy © Jones & 3.Bartlett Edward Learning, Jenner established LLC that disease (smallpox)© Jones12. & Many Bartlett of the advancesLearning, toward LLC understanding molec- NOT FOR SALEcould OR be DISTRIBUTIONprevented through vaccination using a simi-NOT FOR ularSALE biology OR and DISTRIBUTION general principles in biology were lar but milder disease-causing agent. based on experiments using microbial model sys- 4. Semmelweis and Snow believed that infectious dis- tems . ease was caused by particles transmitted from the 13. With the advent of the electron microscope, microbi- environment (not a miasma ) and that disease trans- ologists recognized that there were two basic types mission could be© interruptedJones & throughBartlett simple Learning, mea- LLC of cellular organization:© eukaryotic Jones & and Bartlett prokaryotic Learning, . LLC sures. (Figure 1.4NOT ) FOR SALE OR DISTRIBUTION(Figure 1.10 ) NOT FOR SALE OR DISTRIBUTION 14. Following from the initial work by Ehrlich, antibiot- Concept 1.3 The Classical Golden Age of ics were developed as “magic bullets” to cure many Microbiology Reveals the Germ infectious diseases. 5. Pasteur’s fermentation studies suggested that microorganisms could produce chemical changes. He Concept 1.6 A Third Golden Age of Microbiology ©proposed Jones the& Bartlett germ theory Learning, of disease, LLCwhich stated Is Now © Jones & Bartlett Learning, LLC NOTthat humanFOR infectiousSALE OR disease DISTRIBUTION was due to chemical 15. In the 21st century, fi ghting infectious disease, iden-NOT FOR SALE OR DISTRIBUTION changes brought about by microorganisms infecting tifying emerging and reemerging infectious dis- the body. eases, combating increasing antibiotic resistance , 6. Lister’s use of antisepsis techniques and Pasteur’s countering the bioterrorism threat, and addressing studies of pébrine supported the germ theory and the potential spread of infectious diseases due to © Jones & Bartlettshowed Learning, how diseases LLC could be controlled. © Jones &climate Bartlett change Learning, are challenges LLC facing microbiology, 7. Koch’s work with anthrax and development of pure healthcare systems, and society. NOT FOR SALEcultures OR ledDISTRIBUTION to a method (Koch’s postulates ) to relateNOT FOR16. MicrobialSALE ORecology DISTRIBUTION is providing new clues to the roles a specifi c microorganism to a specifi c disease. of microorganisms in the environment. The under- (Figure 1.7) standing of microbial evolution using modern gene 8. Laboratory science arose as Pasteur and Koch technologies has expanded our understanding of hunted down the microorganisms of infectious dis- microorganism relationships. ease. Pasteur’s lab© Jonesdeveloped & aBartlett vaccine for Learning, human LLC © Jones & Bartlett Learning, LLC rabies. Koch’s lab isolated, cultivated, and identifi ed NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION the pathogens responsible for cholera and tuberculosis.

Chapter selF-test © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC For Steps NOT A–D FOR , you can fi nd answers to questions and problems in SALE OR DISTRIBUTION AppendixNOT D . FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 31 03/04/17 9:16 am 32 CHAPTER 1 MICROBIOLOGY: THEN AND NOW

Multiple Choice © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Read each question carefullyNOT beforeFOR selectingSALE ORthe one DISTRIBUTION answer that best fi ts the question or statement. NOT FOR SALE OR DISTRIBUTION

1. Who was the fi rst person to see bacterial cells with 9. What group of microbial agents would eventually be the microscope? identifi ed from the work of Ivanowsky and Beijerinck? A. Pasteur A. Viruses ©B. Jones Koch & Bartlett Learning, LLC B. Fungi© Jones & Bartlett Learning, LLC C. Leeuwenhoek C. Protists NOTD. Hooke FOR SALE OR DISTRIBUTION D. BacteriaNOT FOR SALE OR DISTRIBUTION 2. What process was studied by Redi and Spallanzani? 10. What microbiological fi eld was established by Wino- A. Spontaneous generation gradsky and Beijerinck? B. Fermentation A. Virology C. Variolation B. Microbial ecology © Jones & BartlettD. Antisepsis Learning, LLC © Jones &C. Bartlett Bacteriology Learning, LLC NOT FOR SALE 3. The ORprocess DISTRIBUTION of _____ involved the inoculation of driedNOT FOR D.SALE Mycology OR DISTRIBUTION smallpox scabs under the skin. 11. What group of microorganisms has a variety of inter- A. vaccination nal cell compartments and many of which act as B. antisepsis decomposers? C. variolation A. Bacteria D. immunization© Jones & Bartlett Learning, LLC B. Viruses © Jones & Bartlett Learning, LLC 4. What is the name for the fi eld of study established by C. Archaea Semmelweis andNOT Snow FORin the mid-1800s?SALE OR DISTRIBUTIOND. Fungi NOT FOR SALE OR DISTRIBUTION A. Immunology 12. Which one of the following organisms was not a B. Bacteriology model organism related to the birth of molecular C. Virology genetics? D. Epidemiology A. Streptococcus 5. © The Jones process & ofBartlett controlled Learning, heating, called LLC _____, was B. ©Penicillium Jones & Bartlett Learning, LLC NOTused toFOR keep SALE wine from OR spoiling. DISTRIBUTION C. NOTEscherichia FOR SALE OR DISTRIBUTION A. curdling D. Neurospora B. fermentation 13. Which group of microbial agents is eukaryotic? C. pasteurization A. Bacteria D. variolation B. Viruses 6. What surgical practice was established by Lister? C. Archaea © Jones & BartlettA. Antisepsis Learning, LLC © Jones &D. Bartlett Algae Learning, LLC NOT FOR SALEB. OR Chemotherapy DISTRIBUTION NOT FOR 14. TheSALE term _____OR DISTRIBUTIONwas used to refer to antimicrobial sub- C. Variolation stances naturally derived from some _____. D. Sterilization A. antibiotic; bacteria and fungi 7. Which one of the following statements is not part of B. antisepsis; other living organisms Koch’s postulates? C. antibiotic; viruses A. The microorganism© Jones must & Bartlettbe isolated Learning, from a LLC D. fermentation; microbes © Jones & Bartlett Learning, LLC dead animalNOT and pure FOR cultured. SALE OR DISTRIBUTION 15. Which one of the followingNOT FORis not SALE considered OR anDISTRIBUTION B. The microorganism and disease can be identifi ed emerging infectious disease? from a mixed culture. A. Polio C. The pure cultured organism is inoculated into a B. SARS healthy, susceptible animal. C. Lyme disease D. The same microorganism must be present in D. AIDS © Jonesevery case& Bartlett of the disease. Learning, LLC 16. What© strategy Jones is ¬ Bartlett part of evolutionary Learning, medicine? LLC 8. NOT Match the lab with the correct set of identifi ed dis- FOR SALE OR DISTRIBUTION A. NOT Understanding FOR SALE the role OR of the DISTRIBUTION human microbiome eases. B. Understanding how life began on Earth A. Pasteur: tetanus and tuberculosis C. Reducing the emergence of infectious diseases B. Koch: anthrax and rabies D. Stimulating the development of antimicrobial C. Koch: cholera and tuberculosis drugs © Jones & BartlettD. Pasteur: Learning, diphtheria LLC and typhoid fever © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

9781284101041_CH01_001_034.indd 32 03/04/17 9:16 am Step C: Applications and Problem Solving 33

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION True–False Each of the following statements is true (T ) or false (F ). If the statement is false, substitute a word or phrase for the underlined word or phrase to make the statement true. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 17. _____ LeeuwenhoekNOT believed FOR that SALE animalcules OR DISTRIBUTION arose 21. _____ Koch proposed theNOT germ FOR theory. SALE OR DISTRIBUTION spontaneously from decaying matter. 22. _____ Variolation involved inoculating individuals with 18. _____ Semmelweis proposed that cholera was a smallpox scabs. waterborne disease. 23. _____ Most microbes today exist as independent, 19. _____ Some bacterial cells can convert nitrogen gas free-living cells.

(N2 ) into ammonia (NH 3 ). 24. _____ Pasteur proposed that “wine disease” was a 20. © _____ Jones Fungi & are Bartlett eukaryotic Learning, microorganisms, LLC some of souring© Jones of wine caused & Bartlett by yeast Learning, cells. LLC NOTwhich FOR are decomposers. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

step B: ConCept reVieW

© Jones & 25. Bartlett Describe Learning, the concept LLC of spontaneous generation and© Jones 28. & Provide evidence to support the statement: “Not all Bartlett Learning, LLC distinguish between the experiments that supported microbes cause disease; many play important roles NOT FOR SALEand OR refuted DISTRIBUTION the belief. (Key Concept 1.1 ) NOT FOR in the environment.” ( SALE OR DISTRIBUTIONKey Concept 1.4 ) 26. Compare Jenner’s work on smallpox and Pasteur’s 29. Distinguish between the “new generation” of sci- studies on rabies to the concept of preventing dis- entists in the second Golden Age of microbiology ease through vaccination. ( Key Concepts 1.2 and 1.3 ) that set the stage for the antibiotic revolution. ( Key 27. Judge the importance of (a) the germ theory of dis- Concept 1.5 ) ease and (b) Koch’s© Jones postulates & to Bartlett the identifi cation Learning, LLC 30. Assess the importance© Jones of microbial & Bartlett ecology Learning, and LLC of microbes as NOTagents FOR of infectious SALE disease.OR DISTRIBUTION (Key microbial evolution toNOT the currentFOR SALEGolden ORAge DISTRIBUTIONof Concept 1.3 ) microbiology. (Key Concept 1.6 )

step C: appliCations anD proBleM solVinG © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 31. As a microbiologist in the 1940s, you are interested 33. One of the foundations of scientifi c inquiry is proper NOTin discovering FOR SALE new antibiotics OR DISTRIBUTION that will kill bacterial experimentalNOT FOR design SALE involving OR theDISTRIBUTION use of controls. pathogens. You have been given a liquid sample of What is the role of a control in an experiment? For a chemical substance to test in order to determine each of the experiments described in the section on if it kills bacterial cells. Drawing on the culture tech- spontaneous generation, identify the control(s) and niques of Robert Koch, design an experiment that explain how the interpretation of the experimental © Jones & Bartlettwould allow Learning, you to determine LLC the killing properties of© Jones &results Bartlett would Learning, change without LLC such controls. the sample substance. 34. You isolate and pure culture a bacterial organism NOT FOR 32.SALE As aOR microbial DISTRIBUTION ecologist, you discover a new speciesNOT FOR fromSALE ill humans OR DISTRIBUTION that you believe causes the disease. of microbe. How could you determine if it has a pro- However, you cannot fi nd a susceptible animal for karyotic or eukaryotic cell structure? Suppose that it testing that contracts the disease. What would you has a eukaryotic structure. What information would conclude from these observations? be needed to determine if it is a member of the pro- tista or fungi? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

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35. Many people are fond of pinpointing events that alter 37. When you tell a friend that you are taking microbiol- the course of history.© Jones In your mind,& Bartlett which single Learning, event LLC ogy this semester, she asks, “ © JonesExactly & whatBartlett is microbi- Learning, LLC described in this chapter had the greatest infl uence NOT FOR SALE OR DISTRIBUTIONology? ” How do you answer her? NOT FOR SALE OR DISTRIBUTION on (a) the development of microbiology and (b) medi- 38. As microbiologists continue to explore the microbial cine? universe, it is becoming more apparent that microbes 36. Louis Pasteur once stated, “In the fi eld of observa- are “invisible emperors” that rule the world. Now that tion, chance favors only the prepared mind.” How you have completed this chapter, provide examples does this quote apply to the work done by (a) Sem- to support the statement: Microbes rule! ©melweis, Jones (b) & Snow, Bartlett and (c) Learning, Fleming? LLC 39. Who would you © Jones select as the “fi rst microbiologist”? & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION (a) Leeuwenhoek?NOT FOR SALE(b) Hooke? OR (c) DISTRIBUTION Pasteur and Koch? Support your decision.

Concept Mapping See pages XXXI-XXXII for tips on how to construct a concept map. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR 40.SALE Construct OR DISTRIBUTION a concept map for Microbial Agents , usingNOT FOR SALE OR DISTRIBUTION the following terms. Algae Fungi Protists Archaea Microorganisms Protozoa Bacteria Nucleated cells Viruses Decomposers Pathogens© Jones (germs) & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

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