1 Foundations of Microbiology I

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION p a r t Foundations © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 1NOT FOR SALE ofOR DISTRIBUTION MicrobiologyNOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, ChapterLLC 1 Microbiology:© Jones Then & and Bartlett Now Learning, LLC NOT FOR SALE OR DISTRIBUTIONChapter 2 The ChemicalNOT Building FOR SALE Blocks OR of DISTRIBUTIONLife Chapter 3 Concepts and Tools for Studying Microorganisms Chapter 4 Cell Structure and Function in the Bacteria © Jones & Bartlett Learning, LLC © Jonesand &Archaea Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Chapter 5 Microbial Growth and Nutrition Chapter 6 Metabolism of Microorganisms Chapter 7 Control of Microorganisms: Physical and © Jones & Bartlett Learning, LLCChemical Methods © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION n 1676, a century before the Declaration of Independence, a Dutch merchant named Antony van Leeuwenhoek sent a noteworthy letter to the Royal Society of London. Writing in the vernacular of © Jones & Bartlett Learning, LLCI © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONhis home in the United Netherlands,NOT FOR Leeuwenhoek SALE OR described DISTRIBUTION how he used a simple microscope to observe vast populations of minute, living creatures. His reports opened a chapter of science that would evolve into the study of microscopic organisms and the discipline of microbiology. During the next three centuries scientists would discover how profoundly these organisms © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Cells of Vibrio cholerae, transmitted to humans influence the quality of our lives and the environment around us. NOT FORin contaminatedSALE OR water DISTRIBUTION and food, are the cause NOT FOR SALE OR DISTRIBUTION of cholera. We begin our study of the microorganisms by exploring the grassroot developments that led to the establishment of microbiology as a science. These developments are surveyed in Chapter 1, where we focus on some of the individuals who stood at the forefront of discovery.© Today Jones we & are Bartlett in the midstLearning, of a third LLC Golden Age of microbiology© Jones and & our Bartlett understanding Learning, LLC of microorganisms continuesNOT FOR to grow SALE even OR as DISTRIBUTION you read this book. NOT FOR SALE OR DISTRIBUTION Chapter 2 reviews basic chemistry, inasmuch as microbial growth, metabolism, and control are grounded in the molecules and macromolecules these organisms contain and in the biological processes they undergo. Chapter 3 sets down some basic microbiological concepts and describes one of the major tools for studying microorganisms. We will© Jonesconcentrate & Bartlett on the Learning,bacterial organisms LLC in Chapter 4, where© Jones we survey & Bartlett their structural Learning, frameworks. LLC In ChapterNOT 5, weFOR build SALE on these OR frameworksDISTRIBUTION by examining microbial growthNOT FOR patterns SALE and OR nutritional DISTRIBUTION requirements. Chapter 6 describes the metabolism of microbial cells, including those chemical reactions that produce energy and use energy. Part 1 concludes by considering the physical and chemical methods used to control microbial growth and metabolism (Chapter 7). © Jones & BartlettMuch as theLearning, alphabet LLC applies to word development,© Jones in each & Bartlett succeeding Learning, chapters LLC we will formulate words NOT FORinto SALE sentences OR DISTRIBUTIONand sentences into ideas as we constructNOT an FOR understanding SALE OR of DISTRIBUTION microorganisms and concentrate on their importance to public health and human welfare. © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 1 12/19/11 12:49 PM © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Chapter Preview and Key Concepts © Jones & BartlettBeing Learning, a Scientist LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Science may not seem like the most glamorous profession. So, as you read many of the chapters in this text, you might wonder why many scientists have the good fortune to make key discoveries. At times, it might seem like it is © Jones & Bartlett Learning, LLC the luck of the© dra Jonesw, but act & uallyBartlett many Learning,scientists hav LLCe a set of characteristics NOT FOR SALE OR DISTRIBUTION that put themNOT on the FOR trail toSALE success. OR DISTRIBUTION Robert S. Root-Bernstein, a physiology professor at Michigan State University, points out that many prominent scientists like to goof around, play games, and surround themselves with a type of chaos aimed at reveal- © Jones & Bartletting the Learning, unexpected LLC. Their labs may appear to be© Jonesin disorder & ,Bartlett but they knowLearning, LLC NOT FOR SALEexa ORctly DISTRIBUTIONwhere every tube or bottle belongs. ScientistsNOT alsFORo ide SALEntify int ORimately DISTRIBUTION with the organisms or creatures they study (it is said that Louis Pasteur actually dreamed about microorganisms), and this identification brings on an intuition—a “feeling for the organism.” In addition, there is the ability to recognize patterns that might bring a breakthrough. (Pasteur had studied art as a teenager and, © Jones &theref Bartlettore, he Learning,had an appreciati LLCon of patterns.) © Jones & Bartlett Learning, LLC NOT FOR SALEThe gen OReticist DISTRIBUTION and Nobel laureate Barbara McClintockNOT onc FORe rem arked,SALE “I OR was DISTRIBUTION 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 for the unknown. Professor Alcamo once received a letter from a student, asking why he became a microbiologist. © Jones & Bartlett Learning,“It was because LLC I enjoyed my undergraduate© Jones microbiology & Bartlett course” Learning, he said, LLC “and when I needed to NOT FOR SALE OR DISTRIBUTIONselect a graduate major, microbiology seemedNOT likeFOR a good SALE idea. OR I also DISTRIBUTION think I had some of the characteristics described by Root-Bernstein: I loved to try out different projects; my corner of the world qualified as a disaster area; still I was a nut on organization, insisting that all the square pegs fit into the square holes.” For this author, science has been an extraordinary opportunity to discover and understand something© Jones never & bef Bartlettore kno wn.Learning, Science isLLC fun, yet challenging—and© atJones times &ard Bartlettuous, ted ious,Learning, LLC and frustrating.NOT FOR As SALE with most OR of DISTRIBUTION us, we will not make the headlines forNOT a breakthrough FOR SALE discovery OR DISTRIBUTION or find a cure for a disease. However, as scientists we all hope our research will contribute to a better understanding of a biological (or microbiological) phenomenon and will push back the frontiers of knowledge. Like any profession, being a scientist is not for everyone. Besides having a bachelor’s degree in © Jones &biology Bartlett or microbi Learning,ology, youLLC should be well read in the© Jonessciences &and Bartlett capable Learning,of working as LLC part of NOT FORan SALE interdisciplin OR DISTRIBUTIONary team. Of course, you should haveNOT good FORquantitative SALE and OR communicati DISTRIBUTIONon skills, have an inquisitive mind, and be goal oriented. If all this sounds interesting, then maybe you fit the mold of a scientist. Why not consider pursuing a career in microbiology? Some possibilities are described in other Microbiology Pathways included in this book, but you should also visit with your © Jones & Bartlett Learning,instructor .LLC Simply stop by the student© union, Jones buy & two Bartlett cups of Learning,coffee, and you LLC are on your way. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

2 © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 2 12/22/11 11:17 AM © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

© Jones & Bartlett Learning, LLC © JonesChapter & Bartlett Preview Learning, and Key LLCConcepts NOT FOR SALE OR DISTRIBUTION NOT FOR1.1 The SALE Beginnings OR DISTRIBUTION of Microbiology 1. The discovery of microorganisms was Microbiology: dependent on observations made with the microscope. 2. The emergence of experimental science © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning,provided LLC a means to test long-held beliefs Then and Now and resolve controversies. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION MicroInquiry 1: Experimentation and Scientific Inquiry Microbiology is at least as important to the future of the world as any 1.2 Microorganisms and Disease Transmission other branch of science, and more so than most. 3. Early epidemiology studies suggested how —Bernard Dixon (in Animalcules: The Activities, Impacts, and diseases could be spread and be controlled. © Jones & Bartlett Learning, LLC 4. Resistance© Jones to a& disease Bartlett can come Learning, from LLC Investigators of MicrobesNOT [2009]) FOR SALE OR DISTRIBUTION exposureNOT FOR to and recoverySALE fromOR a DISTRIBUTIONmild form of (or a very similar) disease. Space. The final frontier! Really? The final frontier? There are an 1.3 The Classical Golden Age of Microbiology estimated 350 billion large galaxies and more than 1022 stars in the (1854–1914) visible universe. However, the microbial universe consists of more than 5. The germ theory was based on the 31 © Jones & Bartlett Learning, LLC © Jones & Bartlettobservations Learning, that different LLC microorganisms 10 microorganisms scattered among an estimated 2 to 3 billion species. have distinctive and specific roles in nature. So, couldNOT understanding FOR SALE these OR organismsDISTRIBUTION on Earth be as important as NOT FOR SALE6. Antisepsis OR and DISTRIBUTION identification of the cause of studying galaxies in space? animal diseases reinforced the germ theory. In 1990, microbiologist Stephen Giovannoni of Oregon State University 7. Koch’s postulates provided a way to identify a specific microorganism as causing a identified in the Sargasso Sea off the southeast United States what is perhaps specific infectious disease. the most abundant and successful organism on the planet. Called SAR11 8. Laboratory science and teamwork stimulated the © Jones(SAR & Bartlett for Sargasso), Learning, this bacterial LLC organism, which now goes© by Jones the scientific & Bartlett Learning,discovery LLC of additional infectious disease agents. NOT FORname SALE Pelagibacter OR DISTRIBUTION ubique, has been identified across the oceansNOT of theFOR world. SALE OR DISTRIBUTION9. Viruses also can cause disease. What makes it significant is its population size. Estimated to be 2.4 3 1028 10. Many beneficial bacterial species recycle nutrients in the environment. cells, SAR11 alone accounts for 20% of all oceanic bacterial species—and 1.4 Studying Microorganisms 50% of the bacterial species in the surface waters of temperate oceans in 11. The organisms and agents studied in the summer! © Jones & Bartlett Learning, LLC microbiology© Jones represent & Bartlett diverse Learning,groups. LLC SAR11’s success storyNOT suggests FOR the SALE organism OR mustDISTRIBUTION have a significant 1.5 The SecondNOT GoldenFOR SALE Age of MicrobiologyOR DISTRIBUTION impact on the planet. Although such roles remain to be identified and (1943–1970) understood, Giovannoni believes SAR11 is responsible for up to 10% of 12. Microorganisms and viruses can be used as all nutrient recycling on the planet, influencing the cycling of carbon and model systems to study phenomena common to all life. even affecting climate change. 13. All microorganisms have a characteristic cell Also© Jonessailing the & SargassoBartlett Sea Learning, was Craig Venter LLC and his team from the © Jones & Bartlettstructure. Learning, LLC J. CraigNOT Venter FOR Institute. SALE Fresh OR fromDISTRIBUTION his success with the private sector NOT FOR14. SALEAntimicrobial OR DISTRIBUTION chemicals can be effective in effort to sequence the human genome, Venter’s team in 2004 reported treating infectious diseases. the discovery of over 1,800 new microbial species in Sargasso seawater 1.6 The Third Golden Age of Microbiology—Now and from them isolated 1.2 million new gene sequences. 15. Infectious disease (natural and intentional) preoccupies much of microbiology. © Jones & BartlettThen between Learning, 2003 and LLC 2007, Venter’s team sailed© Jones the world’s & Bartlett Learning,16. Microbial LLC ecology and evolution are oceans—à la Charles Darwin—to sample seawater and evaluate the dominant themes in modern microbiology. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION diversity of microorganisms in the Pacific and Atlantic oceans. For the © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION 3

05940_CH01_0001_5thPgs.indd 3 12/19/11 12:50 PM 4 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOTGenome: FOR SALE OR DISTRIBUTIONemerging field of marine molecular microbiology,NOT FOR SALEof nutrients OR DISTRIBUTIONthat form the bodies of all organisms The complete set of Venter believes the gene sequencing of marine and sustaining all the metabolic cycles of life. They genetic information in a cell, organism, or virus. microorganisms will provide examples of novel affect our climate and, as a group, produce about metabolic pathways, identify species that use 50% of the oxygen gas we breathe and many other alternative energy sources, and perhaps help organisms use. They have influenced the evolution solve© critical Jones envir &onmental Bartlett problems, Learning, including LLC of life on Earth and ©actually Jones have & outpacedBartlett that Learning, of LLC climateNOT change. FOR SALE OR DISTRIBUTION the more familiar plantsNOT and FOR animals. SALE OR DISTRIBUTION Giovannoni and Venter are just two of many Microorganisms survive in, or are purposely microbiologists trying to understand the role of put in, many of the foods we eat. Microorganisms microorganisms in the ocean’s ecosystems and and viruses also are in the air we breathe and, © Jones &their Bartlett dominant Learning, role on this LLC planet. But most of at ©times, Jones in the & waterBartlett we drink.Learning, Even closerLLC to NOT FORall, SALE as “Being OR a DISTRIBUTIONScientist” identified, Giovannoni’s home,NOT some FOR 100 SALE billion ORmicroorganisms DISTRIBUTION colonize and Venter’s primary goal is a voyage of discovery. our skin and grow in our mouth, ears, nose, throat, Because only about 1% of the marine microorgan- and digestive tract ( Figure 1.1a ). Fortunately, the isms have been identified, the microbial universe majority of these microbes, called our natural does represent an inner final frontier! microbiota, are actually beneficial in helping us © Jones & Bartlett Learning, LLC © Jones & resistBartlett disease, Learning, and regulating LLC development and NOT FOR SALE OR DISTRIBUTIONThe science of microbiology embracesNOT a biologi FOR SALEnutrition. OR To DISTRIBUTION be human, we must be “infected.” cally diverse group of usually microscopic life When most of us hear the word “bacterium” forms, encompassing primarily microorganisms or “virus” though, we think infection or disease. (bacteria, fungi, and protists) and viruses. Although such pathogens (disease-causing agents) Microorganisms© Jones & Bartlett (or microbes Learning, for short) LLC are are rare, they periodically© Jones have & carved Bartlett out Learning,great LLC swatches of humanity as epidemics passed over presentNOT in vast FOR numbers SALE in ORevery DISTRIBUTION environment and NOT FOR SALE OR DISTRIBUTION habitat on Earth where there is water. They survive the land. Some diseases—such as plague, cholera, in Antarctica, on top of the tallest mountains, near and smallpox—have become known historically thermal vents in the deepest parts of the oceans, as “slate-wipers,” a reference to the barren towns and even miles down within the crust of the earth. they left in their wake (MicroFocus 1.1). Even © Jones &In Bartlettall, microbes Learning, make up more LLC than half of Earth’s today,© Jones with antibiotics & Bartlett and Learning, vaccines to cureLLC and Biomass: NOT FORbiomass SALE. OR DISTRIBUTION preventNOT manyFOR infectious SALE OR diseases, DISTRIBUTION pathogens still The total weight of living The rich diversity of microorganisms is bring concern and sometimes panic. Just think organisms within a defined environment. reflected in their profound influence on all aspects about the scares that AIDS, and most recently of life. Most are harmless or indeed beneficial. avian and swine influenzas have caused worldwide For example, they are essential to the recycling ( Figure 1.1B ). © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

(A) (B) © JonesFigure & Bartlett 1.1 Microbes Learning, Are Key to LLC Health and Illness. (A) Large numbers© Jones of bacterial & Bartlett cells are found Learning, on and in parts LLC of the human body. On the tongue, most are harmless or even beneficial, while a few in our mouth can cause throat infections or lead to tooth decay. NOT FOR(Bar SALE5 5 µm.) OR(B) During DISTRIBUTION the 2009–2010 swine flu pandemic, peopleNOT in affected FOR areas SALE such as OR Mexico DISTRIBUTION wore masks in an attempt to avoid being infected with the virus. © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 4 12/19/11 12:50 PM 1.1 The Beginnings of Microbiology 5

On the last Sunday in August (Plague Sunday), English pilgrims gather in the English countryside outside the village of Eyam,© Jones to pay & homage Bartlett to the Learning, LLC © Jones & Bartlett Learning, LLC townsfolk who in 1665–1666NOT gaveFOR their SALE lives soOR that DISTRIBUTION NOT FOR SALE OR DISTRIBUTION others might live. The pilgrims pause, bow their heads, and remember. In 1665, bubonic plague was raging in London. In late August, a traveling tailor arrived in the village of Eyam, about 140 miles north of London.© Jones Unknown & Bartlett to him, cloth Learning, arriving from LLC © Jones & Bartlett Learning, LLC LondonNOT was FOR infected SALE with plague-carrying OR DISTRIBUTION fleas. NOT FOR SALE OR DISTRIBUTION Within a few days, plague began to spread throughout Eyam and villagers debated whether Mompesson’s well at Eyam in Derbyshire Peak in they should flee north. The village rector realized Great Britain. During the plague, Eyam residents left that if the villagers left, they could spread the coins in the well in exchange for food and medicines. © Jones &plague Bartlett to other Learning, towns and LLCvillages. So, he made a © Jones & Bartlett Learning, LLC NOT FOR passionateSALE OR plea DISTRIBUTION that they stay. After some deep soul-searching,NOT FOR most townsfolkSALE OR resolved DISTRIBUTION to remain, even though they knew that meant many would die. The villagers marked off a circle of stones outside the village limits, and people from the adjacent towns brought food and supplies to the barrier, leaving them there for the self-quarantined villagers (see figure). Finally, in late 1666,© Jones the plague & Bartlett subsided. TheLearning, rector recorded, LLC “Now, blessed be God, all our© fearsJones & Bartlett Learning, LLC are over for none have died of the plague since the eleventh of October and the pest-houses have long been empty.” In the end, 260NOT of the FOR town’s SALE350 residents OR succumbedDISTRIBUTION to the plague. Some have suggestedNOT this FOR SALE OR DISTRIBUTION self-sacrificing incident is commemorated in a familiar children’s nursery rhyme, one version of which is: A ring-a-ring of rosies A pocketful of posies A© tishoo! Jones A tishoo! & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC WeNOT all fall FOR down. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The ring of rosies refers to the rose-shaped splotches on the chest and armpits of plague victims. Posies were tiny flowers the people hoped would sweeten the air and ward off the foul smell associated with the disease. “A tishoo!” refers to the fits of sneezing that accompanied the disease. The last line, the saddest of all, suggests the deaths that befell so many. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Still, if microbes were solely agents of disease, and efforts of so many. Along the way, we con- none of us would be here today. Rather “infec- tinue to see how curiosity and scientific inquiry tion” is a way of life—we, all life, and our planet stimulated the quest for understanding. are dependent on microbes!© Jones & Bartlett Learning,Although LLC the study of microorganisms© Jones began & Bartlett Learning, LLC A major focus of NOTthis introductory FOR SALE chap- OR DISTRIBUTIONin earnest with the work of PasteurNOT and Koch, FOR SALE OR DISTRIBUTION ter is to give you an introspective “first look” at they were not the first to report microorganisms. microbiology—then and now. We will see how To begin our story, we reach back to the 1600s, microbes were first discovered and how those that where we encounter some equally inquisitive cause ©infectious Jones disease& Bartlett preoccupied Learning, the minds LLC individuals. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 1.1 The Beginnings of Microbiology As the 17th century arrived, an observational revo- Many individuals in Holland, England, and Italy lution was about to begin: Dutch spectacle maker, further developed the two-lens system. In fact, © JonesZacharias & Bartlett Janssen, Learning, was one ofLLC several individuals it was© inJones 1625 that& Bartlett the Italian Learning, Francesco StellutiLLC Convex: NOT FORwho SALE discovered OR DISTRIBUTION that if two convex lenses were or GiovanniNOT FOR Faber SALE used theOR term DISTRIBUTION microscopio or Referring to a surface put together, small objects would appear larger. “microscope” to refer to this new invention, which that curves outward. © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 5 12/19/11 12:50 PM 6 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONGalileo had suggested be called, “the NOTsmall glassFOR SALEand Leeuwenhoek OR DISTRIBUTION believed only sound observa- for spying things up close.” This combination of tion and experimentation could be trusted—a lenses, or “compound microscope,” would be the requirement that remains a cornerstone of all sci- forerunner of the modern microscope. ence inquiry today. Leeuwenhoek chose to communicate his © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Microscopy—Discovery observations through letters to England’s Royal of theNOT Very FOR Small SALE OR DISTRIBUTION Society. In 1674, oneNOT letter FOR described SALE a sample OR DISTRIBUTION of

key concept cloudy surface water from a marshy lake. Placing the 1. The discovery of microorganisms was dependent sample before his lens, he described hundreds of on observations made with the microscope. what he thought were tiny, living animals (prob- © Jones & Bartlett Learning, LLC ably© protists),Jones &which Bartlett he called Learning, animalcules LLC. His Robert Hooke, an English natural philosopher NOT FOR SALE OR DISTRIBUTION curiosityNOT aroused,FOR SALE Leeuwenhoek OR DISTRIBUTION soon located even (the term “scientist” was not coined until 1833), smaller animalcules in rainwater, which, reported was one of the most inventive and ingenious in his 18th letter in 1676, likely represent the first minds in the history of science. As the Curator description of bacterial cells. of Experiments for the Royal Society of London, In 1683, he sent his 39th letter to the Royal Hooke was the first to take advantage of the mag- © Jones & Bartlett Learning, LLC © Jones & SocietyBartlett in whichLearning, he described LLC and illustrated for nification abilities of the compound microscope. NOT FOR SALE OR DISTRIBUTION NOT FOR SALEthe first OR time DISTRIBUTION what almost certainly were swim- Although these microscopes only magnified about ming bacterial cells taken from dental plaque 25 times (253), Hooke made detailed studies of ( Figure 1.2E ). Leeuwenhoek wrote: many small living objects. In 1665, the Royal Society published his Micrographia, which con- © Jones & Bartlett Learning, LLC “I then most always© Jones saw, with & Bartlett great won- Learning, LLC tained descriptions of microscopes and stunning der, that in the said matter there were many NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION hand-drawn illustrations, including the anatomy very little living animalcules, very prettily of many insects and the structure of cork, where a-moving. The biggest sort . . . had a very he used the word cella to describe the “great many strong and swift motion, and shot through little boxes” he observed and from which today we the water (or spittle) like a pike does through © Jones &have Bartlett the word Learning, “cell” ( Figure LLC 1.2A ). Importantly, ©the Jones water. The & Bartlettsecond sort Learning, . . . oft-times LLC spun NOT FORHooke SALE was OR the DISTRIBUTION first person to describe and draw a NOTround likeFOR a topSALE . . . and OR these DISTRIBUTION were far more microorganism, a mold he found growing on the in number.” sheepskin cover of a book ( Figure 1.2B ). Micrographia represents one of the most Leeuwenhoek’s sketches were elegant in important books in science history because it detail and clarity. Among the 165 letters sent to © Jones & Bartlett Learning,awakened LLC the learned and general population© Jones & theBartlett Royal Society,Learning, he outlined LLC structural details NOT FOR SALE OR DISTRIBUTIONof Europe to the world of the very small,NOT revo- FOR SALEof yeast ORcells, DISTRIBUTION and described thread-like fungi and lutionized the art of scientific investigation, and microscopic algae. showed that the microscope was an important tool Unfortunately, Leeuwenhoek invited no one for unlocking the secrets of nature. to work with him, nor did he show anyone how he Antony van Leeuwenhoek, a contemporary of ground his lenses. Without these lenses, natural- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Hooke, was a successful tradesman and dry goods ists were hard pressed to repeat his observations dealerNOT in Delft, FOR Holland. SALE As OR a cloth DISTRIBUTION merchant, he or verify his results,NOT which FOR are key SALE components OR DISTRIBUTION of used hand lenses to inspect the quality of cloth. scientific inquiry. In fact, it took Hooke more than After seeing Hooke’s Micrographia, and without a year to develop a microscope that could resolve scientific training, Leeuwenhoek became skilled Leeuwenhoek’s animalcules. Still, Leeuwenhoek’s © Jones &at Bartlettgrinding single Learning, pieces of LLC glass into fine, bicon- observations© Jones on& theBartlett presence Learning, and diversity LLC of his NOT FORvex SALE lenses, OR which DISTRIBUTION he placed between two silver “marvelousNOT FOR beasties” SALE and OR Hooke’s DISTRIBUTION Micrographia or brass plates riveted together ( Figure 1.2C, D ). opened the door to a completely new world: the Using only a single lens, no larger than the head world of the microbe. of a pin, his “simple microscope” could magnify concept and reasoning checks objects more than 2003. 1.1 If you were alive in Leeuwenhoek’s time, how would © Jones & Bartlett Learning,The process LLC of “observation” is an© important Jones & Bartlettyou explain Learning, the origin LLC for the animalcules he saw NOT FOR SALE OR DISTRIBUTIONskill for all scientists, including microbiologists—NOT FOR SALEwith OR his DISTRIBUTIONsimple microscope?

05940_CH01_0001_5thPgs.indd 6 12/19/11 12:50 PM 1.1 The Beginnings of Microbiology 7

(A) (B) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Lens

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

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

Elevating screw © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC (C) (D) (E) Figure 1.2 The First ObservationsNOT FOR and Drawings SALE ofOR Microorganisms. DISTRIBUTION In his Micrographia, Robert HookeNOT included FOR a drawing SALE of thin OR shavings DISTRIBUTION of cork that he saw with his microscope (A). He also described and drew the structure of a fungal mold (B). (C) Leeuwenhoek looking through one of his simple microscopes. (D) For viewing, he placed an object on the tip of the specimen mount, which was attached to a screw plate. An elevating screw moved the specimen up and down while the focusing screw pushed against the metal plate, moving the specimen toward or away from the lens. (E) Leeuwenhoek’s drawings of animalcules (bacterial cells) were included in a letter sent to the Royal Society in 1683. He found many of these organisms© Jonesbetween his & teeth Bartlett and those Learning, of others. LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 7 12/19/11 12:50 PM 8 chapter 1 Microbiology: Then and Now

key concept 2. The emergence of experimental science provided a means to test long-held beliefs and resolve controversies.© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION In the early 1600s, most naturalists were “vital- ists,” individuals who thought life depended on a mysterious “vital force” that pervaded all organisms. This force provided the basis for the doctrine © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC of spontaneous generation, which suggested that NOT FORorganisms SALE OR could DISTRIBUTION arise from nonliving matter; NOT FOR SALE OR DISTRIBUTION that is, where there was putrefaction and decay. Common people embraced the idea, for they too Open jar–maggots Covered jar– appear on meat no maggots witnessed what appeared to be slime that pro- Figure 1.3 Redi’s Experiments Refute Spontaneous © Jones & Bartlett Learning,duced toads LLC and decomposing wheat ©grains Jones that & Bartlett Learning, LLC Generation. Francesco Redi carried out one of the first NOT FOR SALE OR DISTRIBUTIONgenerated wormlike maggots. NOT FOR SALEbiological OR experiments DISTRIBUTION by placing a piece of meat in an Regarding the latter, Leeuwenhoek suggested open jar and another in a jar covered with gauze. Maggots that maggots did not arise from wheat grains, arose only in the open jar because flies had access to the meat where they laid their eggs. but rather from tiny eggs laid in the grain that he could© Jones see with & his Bartlett microscope. Learning, Resolving LLC such © Jones & Bartlett Learning, LLC divergentNOT observations FOR SALE concerning OR DISTRIBUTION spontaneous microscopical animalsNOT of most FOR dimensions.” SALE OR He wasDISTRIBUTION generation required a new form of investigation— convinced that putrefaction could generate the “experimentation”—and a new generation of vital force needed for spontaneous generation. experimental naturalists arose. Because experiments almost always are sub- Noting Leeuwenhoek’s descriptions, the ject to varying interpretations, the Italian cleric © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Italian naturalist Francesco Redi performed one and naturalist Lazzaro Spallanzani challenged NOT FORof SALE history’s OR first DISTRIBUTION controlled biological experiments Needham’sNOT FOR conclusions SALE OR and DISTRIBUTION suggested that the to see if maggots could arise from rotting meat. duration of heating might not have been long In 1668, he covered some jars of rotting meat enough. In 1765, he repeated Needham’s experi- with gauze, thereby preventing the entry of flies, ments by boiling similar flasks for longer periods. © Jones & Bartlett Learning,while leaving LLC other jars uncovered. If© flies Jones were & AsBartlett controls, Learning, he left some LLC tubes open to the air, NOT FOR SALE OR DISTRIBUTIONprevented from entering and landing onNOT pieces FOR of SALEstoppered OR others DISTRIBUTION loosely with corks, and sealed exposed meat, Redi predicted they could not lay others. After two days, the open tubes were swarm- their invisible eggs and no maggots would hatch ing with animalcules, but the stoppered ones had ( Figure 1.3 ). Indeed, that is exactly what Redi many fewer—and the sealed ones contained none. observed and the idea that spontaneous genera- Spallanzani proclaimed, “the number of animalcula tion could© Jones produce & Bartlett larger living Learning, creatures LLC soon developed is proportional© Jones to the communication & Bartlett Learning, with LLC subsided.NOT However, FOR SALE what ORabout DISTRIBUTION the mysterious the external air.” NOT FOR SALE OR DISTRIBUTION and minute animalcules that appeared to straddle Needham and others countered that the boundary between the nonliving and living Spallanzani’s experiments had destroyed the vital world? Could they arise spontaneously? force of life because excessive heating drove off © Jones & BartlettIn 1748, Learning, a British clergyman LLC and naturalist, the© air Jones necessary & Bartlett for life. TheLearning, controversy LLC over NOT FORJohn SALE Needham, OR DISTRIBUTION suggested that the spontaneous spontaneousNOT FOR generation SALE ORof animalcules DISTRIBUTION continued generation of animalcules resulted from a vital into the mid-1800s. To solve the problem, a new force that reorganized the decaying matter from experimental strategy would be needed. more complex organisms. To prove this, Needham To get at a resolution, in 1860 the French boiled several flasks of mutton broth and sealed Academy of Sciences offered a prize for the best © Jones & Bartlett Learning,the flasks withLLC corks. After several days,© Needham Jones & experimentBartlett Learning, to prove or LLC disprove spontaneous NOT FOR SALE OR DISTRIBUTIONproclaimed that the “gravy swarm’d withNOT life, FORwith SALEgeneration. OR LouisDISTRIBUTION Pasteur took up the challenge

05940_CH01_0001_5thPgs.indd 8 12/19/11 12:50 PM 1.2 Microorganisms and Disease Transmission 9

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORand, SALE through OR an DISTRIBUTION elegant series of experiments spontaneousNOT FOR generation SALE that OR had DISTRIBUTION begun two cen- that were a variation of the methods of Needham turies earlier. and Spallanzani, discredited the idea in 1861. However, today there is another form of MicroInquiry 1 outlines the process of scientific “spontaneous generation”—this time occurring inquiry and Pasteur’s winning experiments. in the laboratory (MicroFocus 1.2). © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Although Pasteur’s experiments generated concept and reasoning checks considerable debate forNOT several FOR years, SALE his exact- OR DISTRIBUTION1.2 Evaluate the role of experimentation NOTas an impor- FOR SALE OR DISTRIBUTION ing and carefully designed experiments marked tant skill to the eventual rejection of spontaneous the end of the long and tenacious clashes over generation.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 1.2NOTMicroorganisms FOR SALE OR DISTRIBUTIONand Disease Transmission NOT FOR SALE OR DISTRIBUTION In the 13th century, people knew diseases could Ignaz Semmelweis was a Hungarian obstetri- be transmitted between individuals, so quaran- cian who was shocked by the numbers of pregnant Quarantine: tines were used to combat disease spread. In 1546, women in his hospital who were dying of puer- An enforced isolation of people or animals with a © Jonesthe & ItalianBartlett poet Learning, and naturalist LLC Girolamo Fracostoro peral© fever Jones (a type & Bartlettof blood poisoning Learning, also LLC called highly communicable NOT FORsuggested SALE that OR transmission DISTRIBUTION could occur by direct childbedNOT fever) FOR during SALE labor. OR HeDISTRIBUTION determined the disease. human contact, from lifeless objects like clothing disease was more prevalent and deadly in the ward and eating utensils, or through the air. handled by medical students (29% deaths) than in By the mid-1700s, the prevalent belief among the ward run by midwifery students (3% deaths). naturalists and common people was that disease This comparative study suggested to Semmelweis © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC resulted from an altered chemical quality of the that disease transmission must involve his medical atmosphere or from tinyNOT poisonous FOR SALE particles OR of DISTRIBUTIONstudents and that the source of contagionNOT must FOR be SALE OR DISTRIBUTION decomposed matter in the air, an entity called from cadavers on which the medical students pre- miasma (the word malaria comes from mala aria, viously had been performing autopsies. Midwifery meaning “bad air”). To protect oneself from the students did not work on cadavers. So, in 1847, black plague© Jones in Europe, & Bartlett for example, Learning, plague LLCdoc- Semmelweis directed© his Jones staff to &wash Bartlett their hands Learning, LLC tors oftenNOT wore FOR an elaborate SALE costumeOR DISTRIBUTION they thought in chlorine water beforeNOT entering FOR SALE the maternity OR DISTRIBUTION would protect them from the plague miasma ward ( Figure 1.5A ). Deaths from childbed fever ( Figure 1.4 ). However, as the 19th century unfolded, more scientists relied on keen observations © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC and experimentation as a way of knowing and Leather hat (indicating NOT FORexplaining SALE ORdivergent DISTRIBUTION observations, for contagion NOT FOR SALE OR DISTRIBUTIONa doctor) and disease. Mask with glass eyes and beak containing a Epidemiology—Understanding “protective” perfumed © Jones & Bartlett Learning, LLC ©sponge Jones & Bartlett Learning, LLC Disease Transmission NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION key concept Stick to remove clothes 3. Early epidemiology studies suggested how diseases of a plague victim could be spread and be controlled.

Gloves Epidemiology© Jones, as & applied Bartlett to infectious Learning, diseases, LLC is © Jones & Bartlett Learning, LLC the scientific study from which the source, cause, NOT FOR SALE OR DISTRIBUTION NOT FOR SALEWaxed OR linen DISTRIBUTION robe and mode of transmission of disease can be identified. The first scientific epidemiological studies, Boots carried out by Ignaz Semmelweis and John Snow, were instrumental in suggesting how diseases were © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC transmitted—and how simple measures could Figure 1.4 Dressed for Protection. This dress was thought to protect NOT FORinterrupt SALE transmission. OR DISTRIBUTION a plagueNOT doctor FOR from SALE the air (miasma) OR DISTRIBUTION that caused the plague.

05940_CH01_0001_5thPgs.indd 9 12/19/11 12:50 PM INQUIRY

10 chapter 1 Microbiology: Then and Now

Science certainly is a body of knowledge then put their “pet hypothesis” to the rigorous controls (the comparative as you can see from the thickness© Jones of & testBartlett first. Learning, LLC condition). For© example,Jones in& experimentBartlett 1,Learning, LLC this textbook! However, scienceNOT also FORis SALEPasteur’s OR previous DISTRIBUTION work suggested that the control wasNOT the FORflask left SALE open. ORSuch DISTRIBUTION a process—a way of learning. Often we the purported examples of life arising controls are pivotal when explaining an accept and integrate into our under- spontaneously in meat or vegetable experimental result. Pasteur’s finding standing new information because it broths were simply cases of airborne that no life appeared in the sealed flask appears consistent with what we believe microorganisms in dust landing on a (experiment 2A) is interesting, but tells is true. But, ©are Jones we confident & Bartlett our beliefs Learning, suitable substanceLLC and then multiplying© Jonesus very & little Bartlett by itself. Learning, We only learn LLC are always inNOT line with FOR what SALE is actually OR DISTRIBUTIONin such profusion that they could be seenNOT something FOR SALE by comparing OR DISTRIBUTION this to the true? To test or challenge current beliefs, as a cloudy liquid. broken neck (or tipped flask) where life scientists must present logical arguments quickly appeared. supported by well-designed and carefully Pasteur’s Experiments Also note that the idea of spontane- executed experiments. Pasteur set up a series of experiments to ous generation could not be dismissed © Jones & Bartlett Learning, LLC test the hypothesis that© Jones“Life only & arises Bartlett by justLearning, one experiment LLC (see “His critics” The Components of Scientific Inquiry from other life” (see facing page). NOT FOR SALE OR DISTRIBUTION NOT FOR SALE ORon facing DISTRIBUTION page). Pasteur’s experiments There are many ways of finding out Experiment 1A and 1B: Pasteur required the accumulation of many the answer to a problem. In science, sterilized a meat broth in glass flasks experiments, all of which pointed to the scientific inquiry—or what has been by heating. He then either left the neck same conclusion. called the “scientific method”—is the open to the air (A) or sealed the glass way problems are investigated.© Let’sJones &neck Bartlett (B). Organisms Learning, only LLCappeared Hypothesis an© dJones Theory & Bartlett Learning, LLC understand how scientific inquiry works (turned the broth cloudy) in the open When does a hypothesis become a theory? by following the logic of the experimentsNOT FOR SALEflask. OR DISTRIBUTION The answer isNOT that thereFOR is SALEno set time OR DISTRIBUTION Louis Pasteur published in 1861 to refute Experiment 2A and 2B: Pasteur or amount of evidence that specifies the idea of spontaneous generation. sterilized a meat broth in swan-necked the change from hypothesis to theory. When studying a problem, the inquiry flasks (A), so named because their A theory is defined as a hypothesis that process usually© Jonesbegins with & observationsBartlett Learning,. S-shaped LLC necks resembled a swan’s © Joneshas been & testedBartlett and shownLearning, to be correct LLC For spontaneous generation, Pasteur’s ear- every time by many separate investigators. NOT FOR SALE OR DISTRIBUTIONneck. No organisms appeared, even afterNOT FOR SALE OR DISTRIBUTION lier observations suggested that organisms many days. However, if the neck was So, at some point, sufficient evidence do not appear from nonliving matter (see snapped off or the broth tipped to come exists to say a hypothesis is now a theory. text discussion of the early observations in contact with the neck (B), organisms However, theories are not written in stone. supporting spontaneous generation). (cloudy broth) soon appeared. They are open to further experimentation Next comes the question, which can © Jones & Bartlett Learning, LLC © Jones & Bartlettand Learning, so can be refuted. LLC be asked in many ways but usually as a Analysis of Pasteur’s Experiments As a side note, today a theory often is NOT“what,” FOR “why,”SALE or OR “how” DISTRIBUTION question. For Let’s analyze the experiments.NOT FOR Pasteur SALE ORused DISTRIBUTIONincorrectly in everyday speech and example, “What accounts for the genera- had a preconceived notion of the truth in the news media. In these cases, a theory tion of microorganisms in the beef broth?” and designed experiments to test his is equated incorrectly with a hunch or From the question, various hypotheses hypothesis. In his experiments, only belief—whether or not there is evidence are proposed that might answer the one variable (an adjustable condition) © Jones & Bartlett Learning, LLC to support it.© In Jones science, &a theory Bartlett is a Learning, LLC question. A hypothesis is a provisional changed. In experiment 1, the flask was general set of principles supported by but testable explanation for anNOT observed FOR SALEopen or sealed;OR DISTRIBUTION in experiment 2, the large amountsNOT of experimental FOR SALE evidence. OR DISTRIBUTION phenomenon. In almost any scientific neck was left intact or exposed to the question, several hypotheses can be unsterile air. Pasteur kept all other factors Discussion Point proposed to account for the same the same; that is, the broth was the same Based on Pasteur’s experiments, could one still argue that spontaneous generation observation.© However, Jones previous& Bartlett work Learning,or in each experiment;LLC it was heated the © Jones & Bartlett Learning, LLC observations usually bias which hypoth- same length of time; and similar flasks could occur? Explain. Also see end of esis looks mostNOT promising, FOR SALE and scientists OR DISTRIBUTION were used. Thus, the experiments had NOTchapter FOR questionSALE 37.OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 10 12/19/11 12:50 PM INQUIRY

1.2 Microorganisms and Disease Transmission 11

© Jones & Bartlett Learning,Flask openLLC Pasteur:© Jones The broth & provides Bartlett Learning, LLC to air nutrients for the growth of NOT FOR SALE OR DISTRIBUTION unseenNOT organisms FOR inSALE the OR DISTRIBUTION air: life comes from other life. Time passes His critics: The decomposed products in the broth give rise to life © Jones & Bartlett Learning,(A) LLC © Jones & throughBartlett spontaneous Learning, generation. LLC Sterile broth Organisms appear NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Each experiment Flask sealed begins with sterilized Pasteur: The heat has killed broth. Any living agents the microorganisms in the air. the broth may have contained have been Time passes His critics: Sealing the flask

© Jones & Bartlett Learning,destroyed by heat.LLC Experiment 1 © Jones & Bartlett Learning,prevents LLCentry of the "life NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONforce” needed for spontaneous generation. (B) Sterile broth No organisms appear

(A) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC

NOT FOR SALE OR DISTRIBUTIONTime Sterile broth NoNOT organisms FOR SALE OR DISTRIBUTION passes appear Flask tilted so broth enters neck

Time

(B)

Organisms© Jones appear & Bartlett Learning, LLC Organisms© Jones appear & Bartlett Learning, LLC after neck after tilting snappedNOT off FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Pasteur: No life will appear in the flask © JonesPasteur & andBartlett the Spontaneous Learning, Generation LLC Controversy. © Jonesbecause µorganisms Bartlett Learning,will not be able to LLC NOT (1A)FOR When SALE a flask OR of sterilized DISTRIBUTION broth is left open to the air, organisms NOTreach FOR the broth. SALE OR DISTRIBUTION appear. (1B) When a flask of broth is boiled and sealed, no organisms His critics: If the “life force” has free access to appear. (2A) Broth sterilized in a swan-necked flask is left open to the the flask, life will appear, given enough time. air. The curvature of the neck traps dust particles and microorganisms, preventing them from reaching the broth. (2B) If the neck is snapped Many days later the intact flask is still free of off to allow in air or the flask is tipped so broth enters the neck, organ- any life. Pasteur has refuted the doctrine of © Jones & Bartlettisms Learning, come in contact LLC with the broth and grow. © Jones & Bartlettspontaneous Learning, generation. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 11 12/19/11 12:50 PM 12 chapter 1 Microbiology: Then and Now

Those who believed in spontaneous generation proposed that animalcules arose from the rearrangement of molecules released from decayed organisms. Today, a different kind of rearrangement of molecules© Jones is occurring. & Bartlett The field, Learning, called synthetic LLC biology, aims to rebuild© or Jones create new & Bartlett“life forms” Learning, LLC (suchNOT as virusesFOR orSALE bacterial OR cells) DISTRIBUTION from scratch by recombining molecules NOTtaken fromFOR different SALE spe- OR DISTRIBUTION cies. It is like fashioning a new car by taking various parts from a Ford and Chevy, and assembling them on a Toyota chassis. In 2002, scientists at the State University of New York, Stony Brook, reconstructed a poliovirus by assembling separate poliovirus genes and proteins (see figure A). A year later, Craig Venter and © Jones & hisBartlett group assembled Learning, a bacteriophage—a LLC virus that infects© Jones bacterial & cells—from Bartlett “off-the-shelfLearning, ”LLC NOT FOR SALEbiomolecules. OR DISTRIBUTION Although many might not consider virusesNOT to be FOR “living” SALE microbes, OR these DISTRIBUTION construc- tions showed the feasibility of the idea. Then in 2004, researchers at Rockefeller University created small “vesicle bioreactors” that resembled crude biological cells (see figure B). The vesicle walls were made of egg white and the cell contents, stripped of any genetic material, were derived from a © Jones & Bartlett Learning,bacterial LLC cell. The researchers then added© Jones genetic &material Bartlett and viralLearning, enzymes, LLCwhich resulted in the cell making proteins, just as in a live cell. NOT FOR SALE OR DISTRIBUTIONImportantly, these steps toward syntheticNOT lifeFOR have SALE more uses OR than DISTRIBUTION simply trying to build something like a bacterial cell from scratch. Design and construction of novel organisms or viruses would have functions very different from naturally occurring organisms. As such, they represent the opportunity to expand evolution’s repertoire by designing cells or organisms that are better at doing certain jobs. Can we,© for Jones example, & design Bartlett bacterial Learning, cells that areLLC better at degrading toxic wastes,© Jones providing & Bartlettalternative Learning, LLC energy sources, or making cheaper pharmaceuticals? These and many other positive benefits are envi- sionedNOT as FORoutcomes SALE of synthetic OR DISTRIBUTION biology. NOT FOR SALE OR DISTRIBUTION Part II of Generating Life appears in Chapter 2 (page 56).

©(A) Jones & Bartlett Learning, LLC (B) © Jones & Bartlett Learning, LLC (A) This image shows naturally occurring polioviruses, similar to those assembled from the individual parts. (BarNOT = 100 nm.)FOR (B )SALE A “vesicle OR bioreactor” DISTRIBUTION that simulates a crude cell was assembledNOT from variousFOR partsSALE of several OR DISTRIBUTION organisms. The green glow is from a protein produced by the genetic material added to the vesicle. (Bar = 10 µm.)

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORdropped, SALE OR showing DISTRIBUTION that disease spread could be theNOT first FORthorough SALE epidemiological OR DISTRIBUTION studies by interrupted. Unfortunately, few physicians initially interviewing sick and healthy Londoners and heeded Semmelweis’ recommendations. plotting the location of each cholera case on a In 1854, a cholera epidemic hit London’s district map ( Figure 1.5B ). The results indicated Soho district. With residents dying, English most cholera cases were linked to a sewage- © Jones & Bartlett Learning,surgeon John LLC Snow set out to discover© Jonesthe rea- & contaminatedBartlett Learning, street pump LLC from which many NOT FOR SALE OR DISTRIBUTIONson for cholera’s spread. He carried NOTout one FOR of SALElocal residents OR DISTRIBUTION obtained their drinking water.

05940_CH01_0001_5thPgs.indd 12 12/19/11 12:50 PM 1.2 Microorganisms and Disease Transmission 13

Figure 1.5 Blocking Disease Transmission. (A) Semmelweis (background, center-left) believed if hospital staff washed their hands, cases of© puerperal Jones fever & Bartlettwould be reduced Learning, by preventing LLC its spread from staff to patients.© Jones & Bartlett Learning, LLC (B) John Snow (inset) producedNOT a map FOR plotting SALE all the OR cholera DISTRIBUTION cases in the London Soho district and observedNOT FOR SALE OR DISTRIBUTION a cluster near to the Broad Street pump (circle).

Snow then instituted the first known example Variolation and Vaccination— of a public© Jones health & measure Bartlett to Learning,interrupt disease LLC Prevention of Infectious© Jones Disease & Bartlett Learning, LLC

transmission—heNOT FOR requestedSALE OR the DISTRIBUTION parish Board of key concept NOT FOR SALE OR DISTRIBUTION Guardians to remove the street pump handle! 4. Resistance to a disease can come from exposure to and Again, disease spread was broken by a simple recovery from a mild form of (or a very similar) disease. procedure. Snow went on to propose that cholera was not © Jones & Bartlett Learning, LLC Besides© Jones the controversies & Bartlett over Learning, the mechanism LLC of inhaled as a miasma but rather was waterborne. In disease transmission, ways to prevent disease from NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION fact, he asserted that “organized particles” caused occurring were being considered. In the 1700s, cholera—an educated guess that proved to be smallpox was prevalent throughout Europe. In correct even though the causative agent would England, for example, smallpox epidemics were not be identified for another 29 years. so severe that one third of the children died before It is important to ©realize Jones that & although Bartlett the Learning, reaching theLLC age of three. Many victims© who Jones recov- & Bartlett Learning, LLC miasma premise was incorrect,NOT FOR the factSALE that OR dis- DISTRIBUTIONered were blinded from corneal infectionsNOT FOR and SALE OR DISTRIBUTION ease was associated with bad air and filth led to most were left pockmarked. new hygiene measures, such as cleaning streets, Significantly, survivors were protected from laying new sewer lines in cities, and improving suffering the disease a second time. These observa- working conditions. These changes helped usher © Jones & Bartlett Learning, LLC tions suggested that if© one Jones contracted & Bartlett a weakened Learning, LLC in the Sanitary Movement and create the infra- NOT FOR SALE OR DISTRIBUTIONor mild form of the NOTdisease, FOR perhaps SALE such OR indi DISTRIBUTION structure for the public health systems we have viduals would have lifelong resistance. today (MicroFocus 1.3). In the 14th century, the Chinese knew that

concept and reasoning checks smallpox survivors would not get reinfected. 1.3 Contrast the importance of the observations and Spreading from China to India and Africa, the © Jones & Bartlettstudies by Learning,Semmelweis and LLC Snow toward providing practice© Jones of variolation & Bartlett developed, Learning, which involved LLC NOT FOR SALEa better OR understanding DISTRIBUTION of disease transmission. blowingNOT a FOR ground SALE smallpox OR DISTRIBUTION powder into the

05940_CH01_0001_5thPgs.indd 13 12/19/11 12:50 PM 14 chapter 1 Microbiology: Then and Now

Today, we have a good grasp of disease transmission mechanisms, as we will discuss in Chapter 13. However,© Jones even with& Bartlett the advances Learning, in sanitation LLC © Jones & Bartlett Learning, LLC andNOT public FOR health, SALE cholera ORremains DISTRIBUTION a public health NOT FOR SALE OR DISTRIBUTION threat in parts of the developing world. In addition, almost 160 years after Semmelweis’ sugges- tions, a lack of hand washing by hospital staff, even in developed nations, remains a major © Jones & mechanismBartlett Learning,for disease transmission LLC (see figure). © Jones & Bartlett Learning, LLC NOT FOR SALEThe simple OR process DISTRIBUTION of washing one’s hands still NOT FOR SALE OR DISTRIBUTION could reduce substantially disease transmission among the public and in hospitals. Two of the most important epidemiological organizations today are the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia, and, © Jones & Bartlett Learning,on a global LLC level, the World Health Organization© Jones (WHO) & Bartlett in Geneva, Learning, Switzerland. LLC Both employ numer- NOT FOR SALE OR DISTRIBUTIONous epidemiologists, popularly called “diseaseNOT FOR detectives,” SALE who, OR like DISTRIBUTION Snow (but with more expertise), systematically gather information about disease outbreaks in an effort to discover how the disease agent is introduced, how it is spread in a community or population, and how the spread can be stopped. For example, in 2008 more than 1,400 people in 43 states developed similar gastrointestinal symptoms, which CDC investigators traced to bacterial contamination in imported jalapeño peppers. Warnings© Jones to not & purchase Bartlett or eatLearning, these peppers LLC halted the outbreak and prevented© Jones further & Bartletttransmis- Learning, LLC sion.NOT And FORto think, SALE it all startedOR DISTRIBUTION with the seminal work of Semmelweis andNOT Snow. FOR SALE OR DISTRIBUTION

individual’s nose. By the 18th century, Europeans technique of vaccination (vacca = “cow”) worked © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC were inoculating dried smallpox scabs under the in all cases and eliminated the risks associated with NOT FORskin SALE of the OR arm. DISTRIBUTION Although some individuals did get variolation.NOT FOR In 1798, SALE he ORpublished DISTRIBUTION a pamphlet on smallpox, most contracted a mild form of the dis- his work that generated considerable interest. ease and, upon recovery, were resistant to future Prominent physicians confirmed his findings, and smallpox infections. within a few years, Jenner’s method of vaccination © Jones & Bartlett Learning,As an LLCEnglish country surgeon, Edward© Jones Jenner & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONlearned that milkmaids who occasionallyNOT con-FOR SALE OR DISTRIBUTION tracted cowpox, a disease of the udders of cows, would subsequently be protected from deadly smallpox. Jenner wondered if intentionally giving cowpox to people would protect them against smallpox© Jones and be an& Bartletteffective alternative Learning, to variola- LLC © Jones & Bartlett Learning, LLC tion. NOTIn 1796, FOR he putSALE the matter OR DISTRIBUTION to the test. NOT FOR SALE OR DISTRIBUTION A dairy maid named Sarah Nelmes came to his office, the lesions of cowpox evident on her hand. Jenner took material from the lesions and scratched © Jones &it Bartlettinto the skin Learning, of a boy LLCnamed James Phipps © Jones & Bartlett Learning, LLC NOT FOR( SALEFigure 1.6 OR). The DISTRIBUTION boy soon developed a slight fever, NOT FOR SALE OR DISTRIBUTION but recovered. Six weeks later Jenner inoculated young Phipps with material from a smallpox lesion. Within days, the boy developed a reaction at the site Figure 1.6 The First Vaccination Against but failed to show any sign of smallpox. Smallpox. Edward Jenner performed the first vaccination © Jones & Bartlett Learning, LLC © Jones & againstBartlett smallpox. Learning, On May 14, LLC1796, material from a cowpox Jenner repeated his experiments with other lesion was scratched into the arm of eight-year-old James NOT FOR SALE OR DISTRIBUTIONchildren, including his own son. His therapeuticNOT FOR SALEPhipps. The OR vaccination DISTRIBUTION protected him from smallpox.

05940_CH01_0001_5thPgs.indd 14 12/19/11 12:50 PM 1.3 The Classical Golden Age of Microbiology (1854–1914) 15

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORspread SALE through OR Europe DISTRIBUTION and abroad. By 1801, some madeNOT in microscope FOR SALE optics OR that allowedDISTRIBUTION better reso- 100,000 people in England had been vaccinated. lution of objects. This resulted in improved and President Thomas Jefferson wrote to Jenner, “You more widespread observations of tiny living organ- have erased from the calendar of human afflictions one isms, many of which resembled short sticks. In fact, of its greatest. Yours is the comfortable reflection that in 1838 the German biologist Christian Ehrenberg mankind can never forget© that Jones you have & lived.”Bartlett Learning,suggested LLC these “rod-like” looking organisms© Jones be & Bartlett Learning, LLC A hundred years wouldNOT pass FOR before SALE scientists OR DISTRIBUTIONcalled bacteria (bakterion = “little rod”).NOT FOR SALE OR DISTRIBUTION discovered the milder cowpox virus was trigger- The Swiss physician Jacob Henle reported in ing a defensive mechanism by the body’s immune 1840 that living organisms could cause disease. system against the deadlier smallpox virus. It is This was strengthened in 1854 by Filippo Pacini’s remarkable© Jones that without & Bartlett any knowledge Learning, of viruses LLC discovery of rod-shaped© Jones cholera & bacteria Bartlett in stool Learning, LLC or diseaseNOT causation, FOR SALE Jenner accomplishedOR DISTRIBUTION what he samples from choleraNOT patients. FOR Still,SALE scientists OR DISTRIBUTION did. Again, hallmarks of a scientist—keen obser- debated whether bacterial organisms could cause vational skills and insight—led to a therapeutic disease because such living organisms sometimes intervention against disease. were found in healthy people. Therefore, how concept and reasoning checks could these bacterial cells possibly cause disease? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 1.4 Evaluate the effectiveness of variolation and vac- To understand clearly the nature of infectious NOT FOR SALEcination OR as ways DISTRIBUTION to produce disease resistance. disease,NOT a new FOR conception SALE ofOR disease DISTRIBUTION had to emerge. In doing so, it would be necessary to demonstrate The Stage Is Set that a specific bacterial species was associated with a During the early years of the 1800s, several events specific infectious disease. This would require some occurred that helped set© the Jones stage for& Bartlettthe coming Learning, very insightful LLC work, guided by Louis© Pasteur Jones in & Bartlett Learning, LLC “germ revolution.” In theNOT 1830s, FOR advances SALE ORwere DISTRIBUTIONFrance and Robert Koch in Germany. NOT FOR SALE OR DISTRIBUTION

1.3 The Classical Golden Age of Microbiology (1854–1914) © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Beginning around 1854, microbiology blos- Always one to tackle big problems, Pasteur soon somedNOT and continued FOR SALE until OR the adventDISTRIBUTION of World set out to understandNOT the process FOR ofSALE fermentation OR DISTRIBUTION Fermentation: War I. During these 60 years, many branches of and the other processes that can accompany it. The A splitting of sugar molecules into simpler microbiology were established, and the founda prevailing theory held that fermentation was strictly products, including tions were laid for the maturing process that has a chemical reaction. However, Pasteur’s microscope alcohol, acid, and gas © Jonesled & Bartlettto modern Learning, microbiology. LLC We refer to this observations© Jones consistently & Bartlett revealed Learning, large numbers LLC of (CO2). NOT FORperiod SALE as theOR first, DISTRIBUTION or classical, Golden Age of tiny NOTyeast cells FOR in theSALE juice ORthat wereDISTRIBUTION overlooked by microbiology. other scientists. When he mixed yeast in a sugar- water solution, the yeast grew and the quantity of Louis Pasteur Proposes That Germs yeast increased. Yeast must be living organisms and Cause Infectious Disease one of the living “ferments” responsible for the fer- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC key concept mentation process. 5. The germ theory was basedNOT on FOR the observations SALE ORthat DISTRIBUTIONPasteur also demonstrated that wines,NOT beers, FOR SALE OR DISTRIBUTION different microorganisms have distinctive and specific and vinegar each contained different and specific roles in nature. types of microorganisms. For example, in studying a local problem of wine souring, he observed Born in© 1822 Jones in Dôle, & Bartlett France, Louis Learning, Pasteur stud-LLC that only soured wines© Jonescontained & populationsBartlett Learning, of LLC ied chemistryNOT FOR at the SALE École Normale OR DISTRIBUTION Supérieure in bacterial cells. These NOTcells must FOR have SALE contaminated OR DISTRIBUTION Paris and, in 1854, was appointed Professor of a batch of yeast and produced the acids that caused Chemistry at the University of Lille in northern the souring. In addition, Pasteur discovered the France ( Figure 1.7A ). Pasteur was among the first process occurred in the absence of oxygen gas scientists who believed that problems in science ( Figure 1.7B ). © Jonescould & Bartlett be solved Learning, in the laboratory LLC with the results ©Pasteur Jones recommended & Bartlett aLearning, practical solution LLC NOT FORhaving SALE practical OR DISTRIBUTION applications. for theNOT “wine FOR disease” SALE problem: OR DISTRIBUTION heat the wine

05940_CH01_0001_5thPgs.indd 15 12/19/11 12:50 PM 16 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALEif microorganisms OR DISTRIBUTION represented agents of change, perhaps human infections could be caused by those microorganisms that cause disease—germs. In 1857, Pasteur published a short paper on wine souring by bacterial cells in which he © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC implied that germs (bacterial cells) also could be NOT FOR SALE OR DISTRIBUTION related to human illness.NOT FOR Five yearsSALE later, OR after DISTRIBUTION he disproved spontaneous generation, he formu- lated the germ theory of disease, which holds that some microorganisms are responsible for © Jones & Bartlett Learning, LLC infectious© Jones disease. & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION concept and reasoning checks 1.5 Describe how wine fermentation and souring led Pasteur to propose the germ theory.

key concept 6. Antisepsis and identification of the cause of animal © Jones & Bartlett Learning, LLC diseases reinforced© the Jones germ theory. & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Pasteur had reasoned that if microorganisms were acquired from the environment, their spread could be controlled and the chain of disease transmis- © Jones & Bartlett Learning, LLC sion© broken.Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTJoseph FOR Lister SALE was ORProfessor DISTRIBUTION of Surgery at Glasgow Royal Infirmary in Scotland, where more than half his amputation patients died— not from the surgery—but rather from postopera- © Jones & Bartlett Learning, LLC © Jones & tiveBartlett infections. Learning, Hearing LLCof Pasteur’s germ theory, (B) Lister argued that these surgical infections resulted NOT FOR SALE OR DISTRIBUTIONFigure 1.7 Louis Pasteur and FermentationNOT Bacteria. FOR SALE OR DISTRIBUTION (A) Louis Pasteur as a 46-year-old professor of chemistry from living organisms in the air. Knowing that car- at the University of Paris. (B) The following is part of bolic acid had been effective on sewage control, in a description of the living bacterial cells he observed. 1865 he used a carbolic acid spray in surgery and “A most beautiful object: vibrios all in motion, advancing or undulating. They have grown considerably in bulk and on surgical wounds ( Figure 1.8 ). The result was length© since Jones the 11th; & manyBartlett of them Learning, are joined together LLC spectacular—the wounds© Jones healed & Bartlettwithout infec- Learning, LLC in longNOT sinuous FOR chains SALE . . .” Pasteur OR concludedDISTRIBUTION these tion. His techniqueNOT would FOR soon SALEnot only OR revolu- DISTRIBUTION bacterial cells can live without air or free oxygen; in fact, “the presence of gaseous oxygen operates prejudicially tionize medicine and the practice of surgery, but against the movements and activity of those vibrios.” also lead to the practice of antisepsis, the use of chemical methods for disinfection of external liv- © Jones & Bartlett Learning, LLC ing© surfaces, Jones such& Bartlett as the skin Learning, (Chapter 7).LLC Once NOT FORto SALE 55°C after OR fermentationDISTRIBUTION but before aging. His again,NOT practical FOR SALEapplications OR DISTRIBUTIONfrom the laboratory controlled heating technique, known as pas triumphed. teurization, soon was applied to other products, In an effort to familiarize himself with biological especially milk. problems, Pasteur turned his attention to pébrine, a Pasteur’s experiments demonstrated that yeast disease of silkworms. He identified a protist as the © Jones & Bartlett Learning,and bacterial LLC cells are tiny, living factories© inJones which & infectiousBartlett agent Learning, in silkworms LLC and on the mulberry NOT FOR SALE OR DISTRIBUTIONimportant chemical changes take place.NOT Therefore, FOR SALEleaves fed OR to DISTRIBUTIONthe worms. By separating the healthy

05940_CH01_0001_5thPgs.indd 16 12/19/11 12:50 PM 1.3 The Classical Golden Age of Microbiology (1854–1914) 17

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORsilkworms SALE fromOR DISTRIBUTIONthe diseased silkworms and their NOT FOR SALE OR DISTRIBUTION food, he managed to quell the spread of disease. The identification of the pathogen was crucial to supporting the germ theory and Pasteur would never again doubt the ability of microorganisms to cause infectious disease.© Jones Now infectious & Bartlett disease Learning, LLC © Jones & Bartlett Learning, LLC would be his only interest.NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION In 1865, cholera engulfed Paris, killing 200 people a day. Pasteur tried to capture the responsible pathogen by filtering the hospital air and trap- ping the© Jonesbacterial &cells Bartlett in cotton. Learning, Unfortunately, LLC © Jones & Bartlett Learning, LLC PasteurNOT could FOR not grow SALE or separateOR DISTRIBUTION one bacterial NOT FOR SALE OR DISTRIBUTION species apart from the others because his broth cultures allowed the organisms to mix freely. Although Pasteur demonstrated that bacterial Figure 1.8 Lister and Antisepsis. By 1870, Joseph Lister (inset) and his students inoculations made animals ill, he could not pin- were using a carbolic acid spray in surgery and on surgical wounds to prevent © Jonespoint & Bartlett an exact Learning,cause. LLC postoperative© Jones infections. & Bartlett Learning, LLC NOT FOR SALETo completely OR DISTRIBUTION validate the germ theory, what NOT FOR SALE OR DISTRIBUTION was missing was the ability to isolate a specific bacterial species from a diseased individual and the animals and found their blood swarming Broth: demonstrate the isolated organism caused the with the same bacterial cells. He reisolated the A liquid containing same disease. nutrients for microbial © Jones & Bartlett Learning,cells in fresh LLC aqueous humor. The cycle© Joneswas now & Bartlettgrowth. Learning, LLC NOT FOR SALE OR DISTRIBUTIONcomplete. These bacterial cells definitelyNOT were FOR the SALE OR DISTRIBUTION concept and reasoning checks 1.6 Assess Lister’s antisepsis procedures and Pasteur’s causative agent of anthrax. work on pébrine toward supporting the germ When Koch presented his work, scientists theory. were astonished. Here was the verification of the © Jones & Bartlett Learning, LLC germ theory that had© eluded Jones Pasteur. & Bartlett Koch’s pro-Learning, LLC NOT FOR SALE OR DISTRIBUTIONcedures became knownNOT as Koch’s FOR postulatesSALE OR and DISTRIBUTION Robert Koch Formalizes Standards to were quickly adopted as the formalized standards Identify Germs with Infectious Disease for implicating a specific organism to a specific key concept disease ( Figure 1.9B ). 7. Koch’s postulates provided a way to identify a specific microorganism as causing a specific infectious disease. © Jones & Bartlett Learning, LLC Koch© JonesDevelops & BartlettPure Learning, LLC NOT FOR SALE OR DISTRIBUTION CultureNOT TFORechniques SALE OR DISTRIBUTION Robert Koch ( Figure 1.9A ) was a German country Growing bacterial cells in an ox’s eye was not doctor who was well aware of anthrax, a deadly very convenient. Then, in 1880, Koch observed a disease that periodically ravaged cattle and sheep, slice of potato on which small masses of bacterial and could cause disease in humans. cells, which he termed colonies, were growing In 1875, Koch injected© Jones mice with& Bartlett the blood Learning, LLC © Jones & Bartlett Learning, LLC from such diseased sheepNOT and FOR cattle. SALE He thenOR DISTRIBUTIONand multiplying. So, Koch tried addingNOT gelatin FOR to SALE OR DISTRIBUTION performed meticulous autopsies and noted the his broth to prepare a similar solid culture sur- same symptoms in the mice that had appeared face. He then inoculated bacterial cells on the in the sheep and cattle. Next, he isolated from surface and set the dish aside to incubate. Within 24 hours, visible colonies would be growing on the blood© Jones a few rod-shaped& Bartlett bacterialLearning, cells LLC and © Jones & Bartlett Learning, LLC the surface, each colony representing a pure cul grew themNOT inFOR the sterileSALE aqueous OR DISTRIBUTION humor of an NOT FOR SALE OR DISTRIBUTION ox’s eye. With his microscope, Koch watched for ture containing only one bacterial type. By 1884, hours as the bacterial cells multiplied, formed agar replaced gelatin as the preferred solidifying Agar: agent (MicroFocus 1.4). A complex polysaccharide tangled threads, and finally reverted to spores. He derived from marine algae. then took several spores on a sliver of wood and concept and reasoning checks © Jonesinjected & Bartlett them intoLearning, healthy mice. LLC The symptoms of 1.7 ©Why Jones was pure & cultureBartlett crucial Learning, to Koch’s postulates LLC NOT FORanthrax SALE appeared OR DISTRIBUTION within hours. Koch autopsied NOTand the FOR germ theory?SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 17 12/19/11 12:50 PM 18 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Postulate 1 The same microorganisms are present in every case of the disease.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Anthrax bacilli Spore Postulate 2 The microorganisms are isolated from the tissues of a dead © Jones & Bartlett Learning,animal, LLC and a pure © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONculture is prepared. NOT FOR SALE OR DISTRIBUTION Postulate 4 The identical microorganisms are isolated and recultivated from the tissue specimens of the experimental © Jones & Bartlett Learning, LLC © Jones & Bartlett animal.Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Postulate 3 Microorganisms from the pure culture are inoculated © Jones & Bartlett intoLearning, a healthy, susceptible LLC © Jones & Bartlett Learning, LLC (A) animal. The disease is NOT FOR SALE ORreproduced. DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (B) Figure 1.9 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 insert (in the upper right) is a photo of the rod-shaped anthrax bacterial cells. Many rods are swollen with spores (white ovals). © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Competition Fuels the Study The Pasteur Lab. Pasteur continued work of Infectious Disease with anthrax and found that the cells could key concept be trapped on a filter and just a small drop of these © Jones & Bartlett Learning,8. Laboratory LLC science and teamwork stimulated© Jones the dis- & cellsBartlett was sufficient Learning, to kill LLC many animals. These covery of additional infectious disease agents. NOT FOR SALE OR DISTRIBUTION NOT FOR SALEand other OR experiments DISTRIBUTION further validated the germ theory. The period of the 1860s took a toll on Pasteur. One of Pasteur’s more remarkable discover- His father and three of his five children died, and ies was made in 1881. For months, he and his a stroke in 1868 left him partially paralyzed in his coworker Charles Chamberland had been working Attenuate: left arm© Jonesand leg. &However, Bartlett he soonLearning, wrote that LLC the on ways to attenuate© the Jones bacterial & Bartlettcells of chicken Learning, LLC To reduce or weaken. workNOT on silkworms FOR SALE was “a ORgood DISTRIBUTIONpreparation for the cholera using heat,NOT different FOR growth SALE conditions, OR DISTRIBUTION investigations that we are about to undertake.” successive inoculations in animals, and virtually Research studies conducted in a laboratory anything that might damage the cells. Finally, they were becoming the normal method of work. developed a weak strain by suspending the bac- © Jones &Pasteur’s Bartlett lab Learning, and coworkers LLC now were primar- terial© Jonescells in a& mildly Bartlett acidic Learning, medium and LLC allow- NOT FORily SALE interested OR inDISTRIBUTION the mechanism of infection and ingNOT the culture FOR SALEto remain OR undisturbed DISTRIBUTION for a long immunity, and the practical applications that period. When the bacterial cells were inoculated could be derived, while Koch’s lab focused on into chickens and later followed by a dose of lethal procedural methods such as isolation, cultiva- pathogen, the animals did not develop cholera. This tion, and identification of specific pathogens. A attenuation principle is the basis for many vaccines © Jones & Bartlett Learning,competition LLC arose that would last into© theJones next & today.Bartlett Pasteur Learning, also applied LLC the principle to anthrax NOT FOR SALE OR DISTRIBUTIONcentury. NOT FOR SALEin 1881 OR and, DISTRIBUTION in a public demonstration, found he

05940_CH01_0001_5thPgs.indd 18 12/19/11 12:50 PM 1.3 The Classical Golden Age of Microbiology (1854–1914) 19

One of the major developments in microbiology was Robert Koch’s use of a solid culture surface on which bacterial colonies would grow. He accomplished© Jones this by& solidifyingBartlett beef Learning, broth LLC © Jones & Bartlett Learning, LLC with gelatin. When inoculatedNOT FOR onto the SALE surface OR of the DISTRIBUTION nutritious NOT FOR SALE OR DISTRIBUTION medium, bacterial cells grew vigorously at room temperature and produced discrete, visible colonies. On occasion, however, Koch was dismayed to find that the gelatin turned to liquid. It appeared that certain bacterial species ©were Jones producing & Bartletta chemical Learning,substance to digest LLC the gelatin. © Jones & Bartlett Learning, LLC Moreover,NOT gelatin FOR liquefiedSALE atOR the DISTRIBUTION warm incubator temperatures NOT FOR SALE OR DISTRIBUTION commonly used to cultivate certain bacterial species. Walther Hesse, an associate of Koch’s, mentioned the problem to his wife and laboratory assistant, Fanny Eilshemius Hesse. She had a possible solution. For years, she had been © Jones &using Bartlett a seaweed-derived Learning, powder LLC called agar (pronounced © Jones & Bartlett Learning, LLC NOT FOR ah’gar)SALE to OR solidify DISTRIBUTION her jams and jellies. Agar was valuable NOT FOR SALE OR DISTRIBUTION because it mixed easily with most liquids and once gelled, it Fanny Hesse. did not liquefy, even at the warm incubator temperatures. In 1880, Hesse was sufficiently impressed to recommend agar to Koch. Soon Koch was using it routinely to grow bacterial species, and in 1884 he first mentioned agar in his© paper Jones on the & isolationBartlett of Learning,the bacterial organismLLC responsible for tuberculosis.© Jones & Bartlett Learning, LLC It is noteworthy that NOTFanny HesseFOR may SALE have ORbeen DISTRIBUTION among the first Americans (she was originallyNOT FOR SALE OR DISTRIBUTION from New Jersey) to make a significant contribution to microbiology. Another point of interest: The common petri dish (plate) also was invented about this time (1887) by Julius Petri, another of Koch’s assistants.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION could protect sheep against this disease as well ( Figure 1.10 ). Pasteur reached the zenith of his career in 1885 when he successfully immunized a young © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC boy against the dreaded disease rabies. Although NOT FORhe neverSALE could OR culture DISTRIBUTION the causative agent of rabies NOT FOR SALE OR DISTRIBUTION on agar, Pasteur could cultivate it in spinal cord tissue of experimental animals. After his coworker Émile Roux tested the vaccine with success in dogs—all immunized animals© Jones survived & Bartlett a rabies Learning, LLC © Jones & Bartlett Learning, LLC exposure—the ultimateNOT test arrived. FOR SALEA 9-year-old OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION boy, Joseph Meister, had been bitten and mauled by a rabid dog. Pasteur gave the boy the untested (in humans) rabies vaccine (MicroFocus 1.5). The treatment© Jones lasted 10& Bartlettdays and theLearning, boy recovered LLC © Jones & Bartlett Learning, LLC and remainedNOT FOR healthy. SALE The OR rabies DISTRIBUTION vaccine was a NOT FOR SALE OR DISTRIBUTION triumph because it fulfilled his dream of applying the principles of science to practical problems. Such successes helped establish the Pasteur Institute Figure 1.10 The Anthrax Bacterial Cells. A photomicro- in Paris, one of the world’s foremost scientific graph of the anthrax bacterial cells taken by Louis Pasteur in © Jones & Bartlett Learning, LLC 1885.© Pasteur Jones circled & the Bartlett bacilli (the Learning, tiny rods) in tissue LLC and establishments. Pasteur presided over the Institute annotated the photograph, “the parasite of Charbonneuse.” NOT FORuntil SALE his death OR in DISTRIBUTION 1895. (“Charbonneuse”NOT FOR is the SALE French equivalentOR DISTRIBUTION of anthrax.)

05940_CH01_0001_5thPgs.indd 19 12/19/11 12:50 PM 20 chapter 1 Microbiology: Then and Now

The notebooks of Louis Pasteur had been an enduring mystery of science ever since the scientist himself requested his family not to show them to anyone. But in 1964, Pasteur’s last surviving grandson donated© Jones the notebooks & Bartlett to the Learning, National Library LLC in Paris, and after soul-searching© Jones for a decade,& Bartlett the Learning, LLC directorsNOT madeFOR them SALE available OR toDISTRIBUTION a select group of scholars. Among the groupNOT was FOR Gerald SALE Geison ofOR DISTRIBUTION Princeton University. What Geison found stripped away part of the veneration conferred on Pasteur and showed another side to his work. In 1881, Pasteur conducted a trial of his new anthrax vaccine by inoculating half a flock of animals with the vaccine, then exposing the entire flock to the disease. When the vaccinated half survived, © Jones & PasteurBartlett was Learning, showered with LLC accolades. However, Pasteur’s© notebooks, Jones according& Bartlett to Geison, Learning, reveal that LLC NOT FOR SALEhe had preparedOR DISTRIBUTION the vaccine not by his own method, but NOTby a competitor’s. FOR SALE OR DISTRIBUTION Pasteur also apparently sidestepped established protocols when he inoculated two boys with a rabies vaccine before it was tested on animals. Fortunately, the two boys survived, possibly because they were not actually infected or because the vaccine was, indeed, safe and effective. Nevertheless, the untested treatment should not have been used, says Geison. His book, The Private Science of Louis Pasteur © Jones & Bartlett Learning,(Princeton LLC University Press, 1995) places© theJones scientist & Bartlettin a more realistic Learning, light and LLC shows that today’s NOT FOR SALE OR DISTRIBUTIONpressures to succeed in research are littleNOT different FOR than SALE they wereOR moreDISTRIBUTION than a century ago.

The© Jones Koch Lab. & BartlettKoch also Learning, reached the heightLLC Other Global Pioneers© Jones Contribute & Bartlett Learning, LLC of hisNOT influence FOR in theSALE 1880s. OR He DISTRIBUTION developed meth- to New DisciplinesNOT in FORMicrobiology SALE OR DISTRIBUTION

ods for staining bacterial cells and preparing per- key concepts manent visual records. In 1882, he identified and 9. Viruses also can cause disease. grew the bacterium responsible for tuberculosis 10. Many beneficial bacterial species recycle nutrients in (TB) in pure culture. In 1883, he interrupted his the environment. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC work on TB to lead a group of German scientists NOT FORstudying SALE choleraOR DISTRIBUTION in Egypt and India. In both coun- AlthoughNOT FOR the list SALE of identified OR DISTRIBUTION microbes was grow- tries, Koch isolated a comma-shaped bacillus and ing, the agents responsible for diseases such as confirmed John Snow’s suspicion that water is the measles, mumps, smallpox, and yellow fever con- key to transmission. In 1891, as director of Berlin’s tinued to elude identification. In 1892, a Russian © Jones & Bartlett Learning,Institute forLLC Infectious Diseases, Koch© returnedJones & scientist,Bartlett Dimitri Learning, Ivanowsky, LLC used a filter developed by Pasteur’s group to trap what he thought NOT FOR SALE OR DISTRIBUTIONto his work on TB. Unfortunately, hisNOT supposed FOR SALE OR DISTRIBUTION vaccine was a total failure—several people actually were bacterial cells responsible for tobacco mosaic died from the vaccine. Still, his TB studies were disease, which produces mottled and stunted significant and ultimately gained him the 1905 tobacco leaves. Surprisingly, Ivanowsky discov- Nobel Prize in Physiology or Medicine. He died ered that when he applied the liquid that passed of a stroke© Jones in 1910. & Bartlett Learning, LLC through the filter to© healthy Jones tobacco & Bartlett plants, Learning, the LLC TheNOT germ FOR theory SALE set a new OR course DISTRIBUTION for studying leaves became mottledNOT and FOR stunted. SALE Ivanowsky OR DISTRIBUTION and treating infectious disease. The studies carried assumed bacterial cells somehow had slipped out by Pasteur and Koch made the discipline of through the filter. bacteriology, the study of bacterial organisms, a Unaware of Ivanowsky’s work, Martinus well-respected field of study. In fact, a new gen- © Jones & Bartlett Learning, LLC Beijerinck,© Jones a Dutch & Bartlett investigator, Learning, did similar LLC exper- eration of international scientists, including sev- NOT FOR SALE OR DISTRIBUTION imentsNOT in FOR 1899 andSALE suggested OR DISTRIBUTION tobacco mosaic dis- eral from the Pasteur and Koch labs, stepped in to ease was a “contagious, living liquid” that acted expand the work on infectious disease ( table 1.1 ). like a poison or virus (virus = “poison”). In 1898,

concept and reasoning checks the first virus responsible for an animal disease— 1.8 Assess the importance of the science laboratory and hoof-and-mouth disease—was discovered, and in © Jones & Bartlett Learning,teamwork LLC to the increasing identification© ofJones patho- & 1901Bartlett American Learning, Walter ReedLLC concluded that the NOT FOR SALE OR DISTRIBUTIONgenic bacteria. NOT FOR SALEagent responsible OR DISTRIBUTION for yellow fever in humans also

05940_CH01_0001_5thPgs.indd 20 12/19/11 12:50 PM 1.3 The Classical Golden Age of Microbiology (1854–1914) 21

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR TABLESALE OR DISTRIBUTIONTABLE NOT FOR SALE OR DISTRIBUTION 1.1 Other International Scientists and Their Accomplishments During the Classical Golden Age of Microbiology

Investigator (Year) Country Accomplishment © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Otto Obermeier (1868) Germany Observed bacterial cells in relapsing fever patients Ferdinand Cohn (1872)NOT FOR GermanSALEy OR DISTRIBUTIONEstablished bacteriology as a science; producedNOT FOR the SALE OR DISTRIBUTION first bacterial taxonomy scheme Gerhard Hansen (1873) Norway Observed bacterial cells in leprosy patients Albert Neisser (1879) Germany Discovered the bacterium that causes gonorrhea *Charles© Jones Laveran & (1880) Bartlett Learning,France LLC Discovered that malaria© is Jones caused by & a Bartlett protozoan Learning, LLC HansNOT Christian FOR Gram SALE (1884) OR DISTRIBUTIONDenmark Introduced staining systemNOT to FOR identify SALE bacterial OR cells DISTRIBUTION Pasteur Lab Elie Metchnikoff (1884) Ukraine Described phagocytosis TABLE TABLE Émile Roux and Alexandre France Identified the diphtheria toxin Yersin (1888) © Jones &Koch Bartlett Lab Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEFriedrich OR Löeffler DISTRIBUTION (1883) Germany IsolatedNOT the FOR diphtheria SALE bacillus OR DISTRIBUTION Georg Gaffky (1884) Germany Cultivated the typhoid bacillus *Paul Ehrlich (1885) Germany Suggested some dyes might control bacterial infections Shibasaburo Kitasato (1889) Japan Isolated the tetanus bacillus © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Emil von Behring (1890) Germany Developed the diphtheria antitoxin Theodore Escherich (1885)NOT FORGerman SALEy OR DISTRIBUTIONDescribed the bacterium responsible for NOTinfant FOR SALE OR DISTRIBUTION diarrhea Daniel E. Salmon (1886) United States Developed the first heat-killed vaccine Richard Pfeiffer (1892) Germany Identified a bacterial cause of meningitis William© Jones Welch and & Bartlett Learning,United States LLC Isolated the gas gangrene© Jones bacillus & Bartlett Learning, LLC TABLEGeorgeNOT Nuttall FOR (1892) SALE ORTABLE DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Theobald Smith and United States Proved that ticks transmit Texas cattle fever F. Kilbourne (1893) S. Kitasato and Japan Independently discovered the bacterium causing TABLEA. Yersin (1894) TABLEFran ce plague © Jones &Emile Bartlett van Ermengem Learning, (1896) LLC Belgium Identified© Jones the bacterium & Bartlett causing Learning, botulism LLC NOT FOR SALE*Ronald ORRoss DISTRIBUTION(1898) Great Britain ShowedNOT mosquitoes FOR SALE transmit OR malaria DISTRIBUTION to birds Kiyoshi Shiga (1898) Japan Isolated a cause of bacterial dysentery Walter Reed (1901) United States Studied mosquito transmission of yellow fever David Bruce (1903) Great Britain Proved that tsetse flies transmit sleeping sickness Fritz Schaudinn and Germany Discovered the bacterium responsible for syphilis Erich Hoffman (1903)© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC *Jules Bordet and NOT FORFran SALEce OR DISTRIBUTIONCultivated the pertussis bacillus NOT FOR SALE OR DISTRIBUTION Octave Gengou (1906) Albert Calmette and France Developed immunization process for tuberculosis Camille Guérin (1906) Howard Ricketts (1906) United States Proved that ticks transmit Rocky Mountain spotted © Jones & Bartlett Learning, LLC fever © Jones & Bartlett Learning, LLC CharlesNOT Nicolle FOR (1909) SALE OR DISTRIBUTIONFrance Proved that lice transmitNOT typhus FOR fever SALE OR DISTRIBUTION George McCoy and United States Discovered the bacterial cause of tularemia Charles Chapin (1911) *Nobel Prize winners in Physiology or Medicine. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 21 12/19/11 12:50 PM 22 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONwas a virus. With these discoveries, theNOT discipline FOR SALEphysiological OR DISTRIBUTION significance of soil microbes and dis- of virology, the study of viruses, was launched. covering the essential roles microorganisms play While many scientists were advancing medi- in the recycling of matter. cal microbiology, others devoted their research Today, along with Giovannoni and Venter, to the environmental importance of microorgan- many microbiologists continue to search for and isms.© The Jones Russian & Bartlettscientist Sergei Learning, Winogradsky LLC understand the roles© ofJones microorganisms. & Bartlett In Learning, fact, LLC discoveredNOT FORbacterial SALE cells thatOR metabolized DISTRIBUTION sulfur with less than 2% ofNOT all microorganisms FOR SALE onOR Earth DISTRIBUTION and developed the concept of nitrogen fixation, having been identified and many fewer cultured, where bacterial cells convert inert nitrogen gas there is still a lot to be discovered in the microbial (N2) into useable ammonia (NH3). Beijerinck was world!

© Jones &the Bartlett first to obtain Learning, pure cultures LLC of microorganisms concept© Jones and & reasoning Bartlett Learning,checks LLC NOT FORfrom SALE soil and OR water DISTRIBUTION by enriching the growth condi- 1.9 NOTDescribe FOR how SALE viruses ORwere discoveredDISTRIBUTION as disease- tions. Together with Winogradsky, he developed causing agents. many of the laboratory methods essential to the 1.10 Judge the significance of the work pioneered by study of microbial ecology, while revealing the Winogradsky and Beijerinck. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 1.4 Studying Microorganisms NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Besides bacteriology and virology, other disci- By the end of the classical Golden Age of micro- plines also were developing at the beginning of biology, the diversity of microbes included more the 20th century. This included mycology, the than just bacterial species. Let’s briefly survey what study© of Jones fungi; protozoology& Bartlett Learning,, the study LLCof the we know about these© groupsJones today. & Bartlett Learning, LLC animal-likeNOT FORprotists; SALE and phycology OR DISTRIBUTION, the study of Bacteria. It isNOT estimated FOR that SALE there OR may DISTRIBUTION be algae ( Figure 1.11 ). more than 10 million bacterial species. Most The applications of microbiological knowl- are very small, single-celled (unicellular) organ- edge also were important to the development of isms (although some form filaments, and many epidemiology, infection control, and immunol associate in a bacterial mass called a “biofilm”). © Jones &ogy, Bartlett which is Learning, the study of bodilyLLC defenses against The© cells Jones may &be Bartlettspherical, Learning,spiral, or rod-shaped LLC NOT FORmicroorganisms SALE OR DISTRIBUTION and other agents. ( FigureNOT 1.12 FORA ), andSALE they OR lack DISTRIBUTION the cell nucleus and most of the typical cellular compartments typical of other microbes and multicellular organisms. The Spectrum of Microorganisms Some bacterial organisms, like the cyanobacteria, and Viruses Is Diverse carry out photosynthesis ( Figure 1.12B ).

© Jones & Bartlett Learning,key concept LLC © Jones & BartlettBesides Learning, the disease-causing LLC members, some NOT FOR SALE OR DISTRIBUTION11. The organisms and agents studied in microbiologyNOT FOR SALEare responsible OR DISTRIBUTION for food spoilage while others represent diverse groups. are useful in the food industry. Many bacterial

NOT FOR SALE OR DISTRIBUTIONincludes the disciplines of NOT FOR SALE OR DISTRIBUTION

Parasitology Protozoology Phycology

Figure 1.11 Microbiology Disciplines by Organism or Agent Studied. This simple concept map shows the © Jones & Bartlett Learning,relationship LLC between microbiology and the organisms© Jones or agents& Bartlett that make Learning, up the various LLC disciplines. Parasitology is the study of animal parasites. Some of these parasites cause disease in humans, which is why parasitology is NOT FOR SALE OR DISTRIBUTIONincluded with the other disciplines of microbiology.NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 22 12/19/11 12:50 PM 1.4 Studying Microorganisms 23

(A) NOT FOR SALE OR DISTRIBUTION(B) NOT FOR SALE OR DISTRIBUTION

(E) (F) Figure 1.12 Groups of Microorganisms.© Jones & (BartlettA) A bacterial Learning, smear showing LLC the rod shaped cells of Bacillus cereus© Jones & Bartlett Learning, LLC (stained purple), a normal inhabitantNOT FOR of the SALEsoil. (Bar OR= 10 µDISTRIBUTIONm.) (B) Filamentous strands of Anabaena, a cyanobacteriumNOT FOR SALE OR DISTRIBUTION that carries out photosynthesis. (Bar = 100 µm.) (C) Smallpox viruses. (Bar = 100 nm.) (D) A typical blue-gray Penicillium mold growing on a loaf of bread. (E) The colonial green alga, Volvox. (Bar = 300 µm.) (F) The ribbon-like cells of the protist Trypanosoma, the causative agent of African sleeping sickness. (Bar = 10 µm.)

species,© alongJones with & severalBartlett fungi, Learning, are decompos LLC (such as the Yellowstone© Jones hot springs), & Bartlett extremely Learning, LLC ers, organismsNOT FOR that SALE recycle OR nutrients DISTRIBUTION from dead salty (such as the DeadNOT Sea), FOR or SALEextremely OR low DISTRIBUTION organisms. pH (such as acid mine drainage). Adaptations to Archaea. Based on recent biochemical and these environments are partly why they have been molecular studies, many bacterial species have collected into their own unique group. Most bac- been reassigned into another evolutionary group, terial and archaeal species have a rigid cell wall © Jonescalled & Bartlett the Archaea. Learning, Many archaeal LLC species can be through© Jones which &nutrients Bartlett are Learning, absorbed from LLC the NOT FORfound SALE in environments OR DISTRIBUTION that are extremely hot environment.NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 23 12/19/11 12:50 PM 24 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONViruses. Although not correctlyNOT labeled FOR as SALEtheir own OR food DISTRIBUTION supply. If that food supply is a microorganisms, currently there are more than human, disease may result. 3,600 known types of viruses. Viruses are not cell Some fungi provide useful products including ular and cannot be grown in pure culture. They antibiotics, such as penicillin. Others are used in have a core of nucleic acid (DNA or RNA) sur- the food industry to impart distinctive flavors in © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC rounded by a protein coat. Among the features foods such as Roquefort cheeses. Together with usedNOT to identify FOR virusesSALE areOR morphology DISTRIBUTION (size, many bacterial species,NOT numerous FOR SALE molds OR play DISTRIBUTION a shape), genetic material (RNA, DNA), and bio- major role as decomposers. logical properties (organism or tissue infected). Protists. The protists consist mostly of Viruses infect organisms for one reason single-celled organisms. Some are free living © Jones &only—to Bartlett replicate. Learning, Viruses LLC in the air or water, for while© Jones others live& Bartlett in association Learning, with plants LLC or NOT FORexample, SALE ORcannot DISTRIBUTION replicate because they need the animals.NOT FORMovement, SALE if ORpresent, DISTRIBUTION is achieved by metabolic machinery inside a cell. Of the known flagella or cilia, or by a crawling movement. viruses, only a small percentage causes disease in Protists obtain nutrients in different ways. humans. Polio, the flu, measles, AIDS, and small- Some absorb nutrients from the surrounding pox are examples ( Figure 1.12C ). environment or ingest algae and bacterial cells. © Jones & Bartlett Learning,The other LLC group of microbes has a cell© Jones nucleus & TheBartlett unicellular, Learning, colonial, LLC or filamentous algae NOT FOR SALE OR DISTRIBUTIONand a variety of internal cellular compartments.NOT FOR SALEcarry out OR photosynthesis DISTRIBUTION ( Figure 1.12E ). The Many of the organisms are familiar to us. aquatic protists also provide energy and organic Fungi. The fungi include the unicellular compounds for the lower trophic levels of the yeasts and the multicellular mushrooms and molds food web. Some protists are capable of causing ( Figure© Jones1.12D ). About& Bartlett 100,000 Learning, species of LLC fungi diseases in animals,© Jonesincluding & humans;Bartlett theseLearning, LLC have NOTbeen described;FOR SALE however, OR DISTRIBUTION there may be as include malaria, severalNOT typesFOR ofSALE diarrhea, OR andDISTRIBUTION many as 1.5 million species in nature. sleeping sickness ( Figure 1.12F ). Most fungi grow best in warm, moist places and secrete digestive enzymes that break down concept and reasoning checks nutrients into smaller bits that can be absorbed 1.11 Why have microorganisms been separated into a © Jones &easily Bartlett across Learning,a rigid cell wall. LLC Fungi thus live in © Jonesvariety of different& Bartlett groups? Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

1.5 The Second Golden Age of Microbiology (1943–1970) The 1940s brought the birth of molecular genetics to taneous mutations that generate resistance to © Jones & Bartlett Learning,biology. Many LLC biologists focused on understand-© Jones & viralBartlett infection. Learning, Besides LLCthe significance of their NOT FOR SALE OR DISTRIBUTIONing the genetics of organisms, includingNOT the nature FOR SALEfindings OR to microbial DISTRIBUTION genetics, the use of microbial of the genetic material and its regulation. model systems showed to other researchers that microorganisms could be used to study general Molecular Biology Relies principles of biology. on Microorganisms Biologists were quick to jump on the “micro- © Jones & Bartlett Learning, LLC bial bandwagon.” ©Experiments Jones & Bartlettcarried out Learning, by LLC key NOTconcept FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 12. Microorganisms and viruses can be used as model Americans George Beadle and Edward Tatum in systems to study phenomena common to all life. the 1940s ushered in the field of molecular biology by using the fungus Neurospora to show that “one In 1943, the Italian-born microbiologist Salvador gene codes for one enzyme.” Oswald Avery, Colin © Jones &Luria Bartlett and the Learning, German physicist LLC Max Delbrück MacLeod,© Jones and & Maclyn Bartlett McCarty, Learning, working LLC with the NOT FORcarried SALE out OR a series DISTRIBUTION of experiments with bacterial bacterialNOT FORspecies SALE Streptococcus OR DISTRIBUTION pneumoniae, sug- cells and viruses that marked the second Golden gested in 1944 that deoxyribonucleic acid (DNA) Age of microbiology. They used a common gut- is the genetic material in cells. In 1953, American inhabiting bacterium, Escherichia coli, to address biochemist Alfred Hershey and geneticist Martha a basic question regarding evolutionary biology: Chase, using a virus that infects bacterial cells, © JonesMutations: & Bartlett Learning,Do mutations LLC occur spontaneously or© doesJones the & providedBartlett irrefutable Learning, evidence LLC that DNA is the sub- NOTPermanent FOR SALE alterations OR in DISTRIBUTIONenvironment induce them? Luria andNOT Dulbrück FOR SALEstance ofOR the DISTRIBUTION genetic material. These experiments DNA base sequences. showed that bacterial cells could develop spon- and discoveries, which will be discussed in more © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 24 12/19/11 12:50 PM 1.5 The Second Golden Age of Microbiology (1943–1970) 25

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORdetail SALE in Chapter OR DISTRIBUTION 8, placed microbiology in the theseNOT organisms FOR alsoSALE have OR a eukaryotic DISTRIBUTION organiza- middle of the molecular biology revolution. tion. Thus, not only are all plants and animals eukaryotes, so are the microorganisms that com- concept and reasoning checks prise the fungi and protists. 1.12 What roles did microorganisms and viruses play in Studies with the electron microscope revealed understanding general© principles Jones of & biology? Bartlett Learning, LLC © Jones & Bartlett Learning, LLC that bacterial (and archaeal) cells had few of the NOT FOR SALE OR DISTRIBUTIONmembranous compartments typicalNOT of eukary- FOR SALE OR DISTRIBUTION otic cells. They lacked a cell nucleus, indicating Two Types of Cellular Organization the bacterial chromosome (DNA) was not sur- Are Realized rounded by a membrane envelope ( Figure 1.13B ). key concept© Jones & Bartlett Learning, LLC Therefore, members ©of Jonesthe Bacteria & Bartlett and Archaea Learning, LLC 13. AllNOT microorganisms FOR SALE have a characteristic OR DISTRIBUTION cell structure. have a prokaryotic (proNOT = “before”) FOR SALE type of cellularOR DISTRIBUTION organization and represent prokaryotes. (By the The small size of bacterial cells hindered scientists’ way, because viruses lack a cellular organization, abilities to confirm whether these cells were similar they are neither prokaryotes nor eukaryotes.) As to other cellular organisms in organization. In the we will see in Chapter 4, there are many differ- 1940s and 1950s, a new type of microscope—the © Jones & Bartlett Learning, LLC ences© betweenJones bacterial& Bartlett and Learning,archaeal cells, LLC blur- electron microscope—was being developed that NOT FOR SALE OR DISTRIBUTION ring NOTthe use FOR of the SALE term “prokaryote.” OR DISTRIBUTION could magnify objects and cells thousands of times better than typical light microscopes. With the elec- concept and reasoning checks tron microscope, for the first time bacterial cells 1.13 Distinguish between prokaryotic and eukaryotic were seen as being cellular like all other microbes, cells. plants, and animals. However,© Jones studies & showedBartlett that Learning, LLC © Jones & Bartlett Learning, LLC they were organized inNOT a fundamentally FOR SALE different OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION way from other organisms. Antibiotics Are Used It was known that animal and plant cells to Cure Infectious Disease contained a cell nucleus that houses the genetic key concept instructions© Jones in the & form Bartlett of chromosomes Learning, and LLC was 14. Antimicrobial chemicals© Jones can be effective& Bartlett in treating Learning, LLC separatedNOT physically FOR SALE from other OR cellDISTRIBUTION structures by infectious diseases.NOT FOR SALE OR DISTRIBUTION a membrane envelope ( Figure 1.13A ). This type of cellular organization is called eukaryotic (eu = In 1910, another coworker of Koch’s, Paul Ehrlich, “true”; karyon = “nucleus”). Microscope observa- synthesized the first “magic bullet”—a chemical tions of the protists and fungi had revealed that that could kill pathogens without damaging the © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

DNA

DNA in cell nucleus © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

(A) (B) © Jones Figure& Bartlett 1.13 False Learning, Color Images LLC of Eukaryotic and Prokaryotic ©Cells. Jones (A) A scanning& Bartlett electron Learning, microscope image LLC of a eukaryotic cell. All eukaryotes, including the protists and fungi, have their DNA (pink) enclosed in a cell nucleus with NOT FORa membrane SALE envelope.OR DISTRIBUTION (Bar = 3 µm.) (B) A transmission electron microscopeNOT FOR image ofSALE a dividing OR Escherichia DISTRIBUTION coli cell. The DNA (orange) is not surrounded by a membrane. (Bar = 0.5 µm.) © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 25 12/19/11 12:51 PM 26 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONsurrounding tissue. Called salvarsan,NOT Ehrlich FOR SALEAdditional OR DISTRIBUTION magic bullets also were being showed that this arsenic-containing compound discovered. The German chemist Gerhard cured syphilis, a sexually transmitted disease. Domagk discovered a synthetic chemical dye, Antibacterial chemotherapy, the use of anti called prontosil, which was effective in treating microbial chemicals to kill microbes, was born. Streptococcus infections. Examination of soil bac- In© 1928,Jones Alexander & Bartlett Fleming, Learning, a Scottish LLC sci- teria led Selman Waksman© Jones to & the Bartlett discovery Learning, of LLC entist,NOT discovered FOR SALE a mold ORgrowing DISTRIBUTION in one of his actinomycin and streptomycin,NOT FOR SALE the latter OR being DISTRIBUTION bacterial cultures ( Figure 1.14A, B ). His curiosity the first effective agent against tuberculosis. He aroused, Fleming observed that the mold, a spe- coined the term antibiotic to refer to those anti- cies of Penicillium, killed the bacterial cells and microbial substances naturally produced by mold © Jones &colonies Bartlett that Learning,were near the LLC mold. He named the and© bacterial Jones species& Bartlett that inhibitLearning, growth LLC or kill NOT FORantimicrobial SALE OR substanceDISTRIBUTION penicillin and developed otherNOT mi croorganisms.FOR SALE OR DISTRIBUTION an assay for its production. In 1940, biochemists The push to market effective antibiotics Howard Florey and Ernst Chain purified peni- was stimulated by a need to treat potentially cillin and carried out clinical trials that showed deadly infections in casualties of World War II the antimicrobial potential of the natural drug ( Figure 1.14c ). By the 1950s, penicillin and several © Jones & Bartlett Learning,(MicroFocus LLC 1.6). © Jones & additionalBartlett antibioticsLearning, were LLC established treatments NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

(A)

(C) © Jones & Bartlett Learning, LLC Figure 1.14 Fleming© Jones and Penicillin. & Bartlett (A) A painting Learning, LLC NOT FOR SALE OR DISTRIBUTION by Dean Fausett of FlemingNOT inFOR his laboratory. SALE OR DISTRIBUTION (B) Fleming’s notes on the inhibition of bacterial growth by the fungus Penicillium. (C) A World War II poster touting the benefits of penicillin and illustrating the great enthusiasm in the United States for treating infectious diseases in war casualties. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

NOT FOR SALE OR DISTRIBUTION(B) NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 26 12/19/11 12:51 PM 1.6 The Third Golden Age of Microbiology—Now 27

Their timing could not have been worse. Howard Florey, Ernest Chain, Norman Heatley, and others of the team had rediscovered penicillin, purified it, and proved it useful in infected patients. But it was 1939, and German bombs© Jones were falling & Bartlett on London. Learning, This was a dangerous LLC time to be doing research© Jones into & Bartlett Learning, LLC new drugs and medicines.NOT What FOR would SALE they do OR if there DISTRIBUTION was a German invasion of England? If theNOT enemy FOR SALE OR DISTRIBUTION were to learn the secret of penicillin, the team would have to destroy all their work. So, how could they preserve the vital fungus yet keep it from falling into enemy hands? Heatley made a suggestion. Each team member would rub the mold on the inside lining of his coat. The Penicillium mold spores would cling to the rough coat surface where the spores could survive© Jones for years & (if Bartlett necessary) Learning, in a dormant LLC form. If an invasion did occur,© hopefullyJones & at Bartlettleast one Learning, LLC teamNOT member FOR would SALE make ORit to DISTRIBUTIONsafety along with his “moldy coat.” Then,NOT in a safe FOR country SALE the OR DISTRIBUTION spores would be used to start new cultures and the research could continue. Of course, a German invasion of England did not occur, but the plan was an ingenious way to hide the treasured organism. The whole penicillin story is well told in The Mold in Dr. Flory’s Coat by Eric Lax (Henry Holt Publishers, © Jones &2004). Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

in medical practice. In fact, the growing arsenal of bacterial studies was being applied to eukaryotic antibiotics convinced many© Jones that the & ageBartlett of infec- Learning,organisms, LLC especially animals. What was© Jones ignored & Bartlett Learning, LLC tious disease was waning. By the mid-1960s, many was the mounting evidence that bacterial species NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION believed all major infections would soon disappear were becoming resistant to antibiotics.

due to antibiotic chemotherapy. concept and reasoning checks Partly due to the perceived benefits of anti- 1.14 Contrast Ehrlich’s salvarsan and Domagk’s prontosil biotics, interest in microbes was waning by the from those drugs developed by Fleming, Florey and end of© the Jones 1960s &as Bartlettthe knowledge Learning, gained LLCfrom Chain, and Waksman.© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

1.6 T he Third Golden Age of Microbiology—Now Microbiology finds itself on the world stage again, The third Golden Age of microbiology faces several © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC in part from the biotechnology advances made in challenges, many of which still concern the infec- NOT FORthe SALE latter part OR of DISTRIBUTIONthe 20th century. Biotechnology tiousNOT diseases FOR that SALE are responsible OR DISTRIBUTION for 26% of all frequently uses the natural and genetically engi- deaths globally ( Figure 1.15 ). neered abilities of microbial agents to carry out A New Infectious Disease Paradigm. biological processes for industrial/commercial/ Infectious disease remains a major concern medical applications. ©It hasJones revolutionized & Bartlett the Learning, worldwide. LLC Even in the United States,© more Jones than & Bartlett Learning, LLC way microorganisms areNOT genetically FOR SALEmanipulated OR DISTRIBUTION100,000 people die each year from bacterialNOT infec-FOR SALE OR DISTRIBUTION to act as tiny factories producing human proteins, tions, making them the fourth leading cause of such as insulin, or new synthetic vaccines, such as death. In fact, on a global scale, infectious dis- the hepatitis B vaccine. In the latest Golden Age, eases are spreading geographically faster than at microbiology again is making important contribu- any time in history. It is estimated that more than tions to© theJones life sciences & Bartlett and humanity. Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION2.5 billion people traveledNOT byFOR air in SALE 2010, makingOR DISTRIBUTION an outbreak or epidemic in any one part of the Microbiology Continues to Face world only a few airline hours away from becom- Many Challenges ing a potentially dangerous threat in another part

key concept of the world. It is a sobering thought to realize © Jones 15. & BartlettInfectious diseaseLearning, (natural LLC and intentional) pre that ©since Jones 2002, & the Bartlett World HealthLearning, Organization LLC NOT FOR SALEoccupies OR much DISTRIBUTION of microbiology. (WHO)NOT has FOR verified SALE more OR than DISTRIBUTION 1,100 epidemic

05940_CH01_0001_5thPgs.indd 27 12/19/11 12:51 PM 28 chapter 1 Microbiology: Then and Now

Noninfectious causes

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

Tuberculosis

Malaria © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALEMeasles OR DISTRIBUTION Other infectious diseases

Figure 1.15 Global Mortality—All Ages. On a global scale, infectious diseases account for about 26% of all deaths. © Jones & Bartlett Learning,Noninfectious LLC causes include chronic diseases,© injuries, Jones nutritional & Bartlett deficiencies, Learning, and maternal LLC and perinatal conditions. NOT FOR SALE OR DISTRIBUTIONSource: World Health Statistics 2008: World HealthNOT Organization. FOR SALE OR DISTRIBUTION

events worldwide. So, unlike past generations, the more newsworthy have been AIDS, hanta- today’s highly mobile, interdependent, and inter- virus pulmonary syndrome, Lyme disease, mad connected© Jones world & provides Bartlett potential Learning, opportunities LLC cow disease, and most© Jones recently & swine Bartlett flu. There Learning, LLC for theNOT rapid FOR spread SALE of infectious OR DISTRIBUTION diseases. is no cure for any NOTof these. FOR Reemerging SALE OR infec DISTRIBUTION Today, our view of infectious diseases also has tious diseases are ones that have existed in the changed. In Pasteur and Koch’s time, it was mainly past but are now showing a resurgence in inci- a problem of finding the germ that caused a specific dence or a spread in geographic range. Among the disease. Today, new pathogens are being discov- more prominent re-emerging diseases are cholera, © Jones &ered Bartlett that were Learning, never known LLC to be associated with tuberculosis,© Jones dengue & Bartlett fever, and, Learning, for the first LLC time in NOT FORinfectious SALE ORdisease DISTRIBUTION and some of these agents actually theNOT Western FOR Hemisphere, SALE OR West DISTRIBUTION Nile virus disease cause more than one disease. In addition, there are ( Figure 1.16A ). The cause for the resurgence may polymicrobial diseases; that is, diseases caused by be antibiotic resistance or a population of suscep- more than one infectious agent. Even some non tible individuals. Climate change also may become © Jones & Bartlett Learning,infectious LLCdiseases, such as heart disease,© may Jones have & implicatedBartlett Learning,in the upsurge LLC and spread of disease a microbial component that heightens the illness. as more moderate temperatures advance to more NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Emerging and Reemerging Infectious northern and southern latitudes. Diseases. Infectious diseases are not only spread- Increased Antibiotic Resistance. Another ing faster, they appear to be emerging more quickly challenge concerns our increasing inability to than ever before. Since the 1970s, new diseases fight infectious disease because most pathogens have ©been Jones identified & Bartlett at the unprecedented Learning, LLC rate are now resistant to© one Jones or more & Bartlettantibiotics Learning, and LLC of oneNOT or more FOR per SALE year. ORThere DISTRIBUTION are now nearly antibiotic resistanceNOT is developing FOR SALE faster OR than DISTRIBUTION 40 diseases that were unknown a generation ago. new antibiotics are being discovered. Ever since For example, the food chain has undergone con- it was recognized that pathogens could mutate Superbug: siderable and rapid changes over the last 50 years, into “superbugs,” a crusade has been waged to A microbe resistant to becoming highly sophisticated and international. restrain the inappropriate use of these drugs by many antimicrobial© Jones drugs. & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Although the safety of food has dramatically doctors and to educate patients not to demand NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION improved overall, progress is uneven and food- them in uncalled-for situations. borne outbreaks from microbial contamination The challenge facing microbiologists and are common in many countries. The trading of drug companies is to find new and effective contaminated food between countries increases antibiotics to which pathogens will not quickly © Jones & Bartlett Learning,the potential LLC that outbreaks will spread.© Jones & developBartlett resistance Learning, before LLC the current arsenal is NOT FOR SALE OR DISTRIBUTIONEmerging infectious diseases areNOT those FOR that SALEcompletely OR useless.DISTRIBUTION Unfortunately, the growing have recently surfaced in a population. Among threat of antibiotic resistance has been accompanied © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 28 12/19/11 12:51 PM (A)

1.6 The Third Golden Age of Microbiology—Now 29

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION and NOTthe public. FOR Bioterrorism SALE OR involvesDISTRIBUTION the intentional or threatened use of biological agents to cause fear in or actually inflict death or disease upon a large population. Most of the recognized biological agents are microorganisms, viruses, © Jones & Bartlett Learning,or microbial LLC toxins that are bringing© Jonesdiseases & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONlike anthrax, smallpox, and plague backNOT into FOR the SALE OR DISTRIBUTION human psyche ( Figure 1.16B ). To minimize the use of these agents to inflict mass casualties, the chal- (A) lenge to the scientific community and micro- © Jones & Bartlett Learning, LLC biologists is to improve© Jones the ways & Bartlettthat bioterror Learning, LLC NOT FOR SALE OR DISTRIBUTIONagents are detected, NOTdiscover FOR effective SALE measures OR DISTRIBUTION to protect the public, and develop new and effective treatments for individuals or whole populations. If there is anything good to come out of such challenges, it is that we will be better prepared © Jones & Bartlett Learning, LLC for potential© Jones natural & Bartlett emerging Learning, infectious diseaseLLC NOT FOR SALE OR DISTRIBUTION outbreaks,NOT FORwhich SALE initially ORmight DISTRIBUTION be difficult to tell apart from a bioterrorist attack.

concept and reasoning checks 1.15 Describe the natural and intentional disease threats © Jones & Bartlett Learning,challenging LLC microbiology. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Microbial Ecology and Evolution Are Helping to Drive the New Golden Age © Jones & Bartlett Learning, LLC key concept © Jones & Bartlett Learning, LLC 16. Microbial ecology and evolution are dominant themes NOT FOR SALE OR DISTRIBUTION in modern microbiology.NOT FOR SALE OR DISTRIBUTION

(B) Since the time of Pasteur, microbiologists have Figure 1.16 Emerging Disease Threats: Natural and wanted to know how a microbe interacts, survives, Intentional. (A) There have been and will continue to and thrives in the environment. Today, micro © Jonesbe & natur Bartlettal disease Learning, outbreaks. West LLC Nile virus (WNV) is © Jones & Bartlett Learning, LLC biology is less concerned with a specific microbe NOT FORjust SALE one of several OR agentsDISTRIBUTION responsible for emerging or NOT FOR SALE OR DISTRIBUTION reemerging diseases. Methods have been designed that and more concerned with the relationships among individuals can use to protect themselves from mosquitoes microorganisms and with their environment. that spread the WNV. (B) Combating the threat of bioterrorism often requires special equipment and protection Microbial Ecology. Traditional methods of because many agents seen as possible bioweapons could microbial ecology require organisms from an envi- be spread through the air. © Jones & Bartlett Learning,ronment beLLC cultivated in the laboratory© so Jonesthat they & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONcan be characterized and identified. However,NOT FOR up SALE OR DISTRIBUTION by a decline in new drug discovery and an increase to 99% of microorganisms do not grow well in the in the time to develop a drug from discovery to lab (if at all) and therefore could not be studied. market. Thus, antibiotic resistance has become Today, many microbiologists, armed with genetic, a major© healthJones threat & Bartlett and a significant Learning, challenge LLC molecular, and biotechnological© Jones & tools, Bartlett can study Learning, LLC for microbiology today. If actions are not taken to and characterize these uncultured microbes. Such NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION contain and reverse resistance, the world could investigations are producing a new understanding be faced with previously treatable diseases that have of microbial communities and their influence on again become untreatable, as in the days before the ecology of all organisms. SAR11 and the plans antibiotics were developed. of Craig Venter, mentioned in the chapter’s opening © Jones & BartlettBioterrorism. Learning, Perhaps LLCit is the potential mis- piece,© areJones but two & examples.Bartlett Learning, LLC NOT FORuse SALE of microbiology OR DISTRIBUTION that has brought microbiol- NOTToday FORwe are SALElearning OR that DISTRIBUTION most microbes do ogy to the attention of the life science community not act as individual entities; rather, in nature they © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 29 12/19/11 12:51 PM 30 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONsurvive in complex, often polymicrobialNOT commu- FOR SALEplaying ORincreasingly DISTRIBUTION important roles in the health of nities called a biofilm ( Figure 1.17A ). Microbes in the planet as described in Part 6 of this text. biofilms act very differently than individual cells Microbial Evolution. It was Charles Darwin— and can be difficult to treat when biofilms cause another of the scientists in this chapter who infectious disease. If you or someone you know combined observation with a “prepared mind”— has had© Jones a middle & earBartlett infection, Learning, the cause LLCwas a who first described© the Jones principles & Bartlett of evolution, Learning, LLC bacterialNOT biofilm. FOR SALE OR DISTRIBUTION which represents theNOT foundation FOR SALE for all OR biology DISTRIBUTION The discovered versatility of many bacterial and medicine. Bioremediation: and archaeal species is being applied to problems Like all life, microorganisms evolve. Because The use of microor that have the potential to benefit humankind. most have relatively short generation times, they ganisms to remove Bioremediation is one example where the under- represent experimental (model) systems in which or decontaminate© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC toxic materialsNOT in the FORstanding SALE of OR microbial DISTRIBUTION ecology has produced a useful evolutionaryNOT FOR processes SALE canOR be DISTRIBUTION observed directly; environment. outcome ( Figure 1.17B ). Other microbes also are microbial evolution is an experimental science. That makes it possible today to “replay history” by following the accumulation of unpredictable, chance events that lead to evolutionary novelty. © Jones & Bartlett Learning, LLC © Jones & ForBartlett example, Learning, when considering LLC the challenges fac- NOT FOR SALE OR DISTRIBUTION NOT FOR SALEing microbiology OR DISTRIBUTION today, current research is putting together a better understanding of the superfast evolution and spread of antibiotic resistance. It is also helping us better understand the mechanisms © Jones & Bartlett Learning, LLC and evolution of emerging© Jones infectious & Bartlett diseases. Learning, LLC NOT FOR SALE OR DISTRIBUTION Researchers onceNOT thought FOR thatSALE they OR would DISTRIBUTION not be able to work out the evolutionary history of microbes. Today, thanks to the availability of sequenced genomes for groups of related and unre- lated microbes, and new analytical approaches, © Jones & Bartlett Learning, LLC researchers© Jones are & constructingBartlett Learning, a family treeLLC that NOT FOR SALE OR DISTRIBUTION moreNOT clearly FOR illustrates SALE evolutionary OR DISTRIBUTION relationships (Chapter 3). Such developments are giving us a (A) better appreciation for the roles microbes have played and are continuing to play in Earth’s evolu- © Jones & Bartlett Learning, LLC © Jones & tion.Bartlett Indeed, Learning, microbial LLCevolution represents the NOT FOR SALE OR DISTRIBUTION NOT FOR SALEorganization OR DISTRIBUTIONfor the biological and microbiological knowledge contained within this text.

concept and reasoning checks 1.16 Give some examples of how microbial ecology and © Jones & Bartlett Learning, LLC evolution are helping© Jones drive the & new Bartlett Golden Age Learning, of LLC NOT FOR SALE OR DISTRIBUTION microbiology. NOT FOR SALE OR DISTRIBUTION

n In conclusion, microbiology (from then until now) has gone from observing the first bacterial © Jones & Bartlett Learning, LLC cells© (Leeuwenhoek)Jones & Bartlett to identifying Learning, and studyingLLC NOT FOR SALE OR DISTRIBUTION individualNOT FOR microorganisms SALE OR DISTRIBUTION(Pasteur and Koch) to sequencing all species in a sample of seawater (Venter and others). Yet, over these 300+ years, (B) microbiologists have only discovered perhaps Figure 1.17 Microbial Ecology—Biofilms and Bioremediation. (A) The plaque 1% of all microbial species. Microbiology from then © Jones(the brown-colored & Bartlett crust) Learning,typically found onLLC tooth surfaces is an example of a© biofilm. Jones & Bartlett Learning, LLC (B) Microbes can be used to clean up toxic spills. A shoreline coated with oil from an oil until now has come a long way, but has a much NOTspill FOR can be sprayedSALE with OR microorganisms DISTRIBUTION that, along with other measures, helpNOT degrade FOR oil. SALElonger wayOR yetDISTRIBUTION to go.

05940_CH01_0001_5thPgs.indd 30 12/19/11 12:51 PM Learning Objectives 31

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALESUMM ORARY DISTRIBUTION of Key Concepts NOT FOR SALE OR DISTRIBUTION 1.1 The Beginnings of Microbiology vaccines for chicken cholera, animal anthrax, and human 1. The observations with the microscope made by Hooke rabies. Koch’s lab focused on isolation, cultivation, and and especially Leeuwenhoek, who reported the existence identification of pathogens such as those responsible for of animalcules (microorganisms), sparked interest in an cholera and tuberculosis. unknown world ©of microscopicJones & life. Bartlett Learning, LLC 9. Ivanowsky and Beijerinck© Jones provided & Bartlettthe first evidence Learning, for LLC 2. The controversyNOT over spontaneous FOR SALE generation OR DISTRIBUTION initiated the viruses as infectiousNOT agents. FOR SALE OR DISTRIBUTION need for accurate scientific experimentation, which then 10. Winogradsky and Beijerinck were the first to recognize provided the means to refute the concept. the beneficial roles played by microorganisms found in the 1.2 Microorganisms and Disease Transmission environment. 3. Semmelweis and Snow believed that infectious disease 1.4 Studying Microorganisms © Jonescould be &caused Bartlett by something Learning, transmitted LLC from the 11. ©Microbes Jones include & Bartlett the “bacteria” Learning, (Bacteria and LLC Archaea), environment and that the transmission could be viruses, fungi, and protists. NOTinterrupted. FOR SALE OR DISTRIBUTION 1.5 TheNOT Second FOR Golden SALE Age ofOR Microbiology DISTRIBUTION (1943–1970) 4. Edward Jenner determined that disease (smallpox) could 12. Many of the advances toward understanding molecular be prevented through vaccination with a similar but milder biology and general principles in biology were based on disease-causing agent. experiments using microbial model systems. 1.3 The Classical Golden Age of Microbiology (1854–1914) 13. With the advent of the electron microscope, microbiologists © Jones & Bartlett5. Pasteur’s Learning, fermentation LLC experiments indicated that micro© Jones & Bartlettrealized Learning, that there were LLC two basic types of cellular NOT FOR SALEor ORganisms DISTRIBUTION could induce chemical changes. He proposed theNOT FOR SALEorganization: OR DISTRIBUTION eukaryotic and prokaryotic. germ theory of disease, which stated that human disease 14. Following from the initial work by Ehrlich, antibiotics could be due to chemical changes brought about by were developed as “magic bullets” to cure many infectious microorganisms in the body. diseases. 6. Lister’s use of antisepsis techniques and Pasteur’s studies of 1.6 The Third Golden Age of Microbiology—Now pébrine supported the germ theory and showed how diseases 15. In the 21st century, fighting infectious disease, identifying can be controlled.© Jones & Bartlett Learning, LLC emerging and reemerging© Jones infectious & Bartlett diseases Learning,, combating LLC 7. Koch’s work withNOT anthrax FOR allowed SALE him to OR formalize DISTRIBUTION the increasing antibioticNOT resistance, FOR and SALE countering OR the DISTRIBUTION methods (Koch’s postulates) for relating a specific micro bioterrorism threat are challenges facing microbiology, organism to a specific disease. These postulates were only health care systems, and society. valid after he discovered how to make pure cultures of 16. Microbial ecology is providing new clues to the roles of bacterial species. microorganisms in the environment. The understanding 8. Laboratory science arose as Pasteur and Koch hunted of microbial evolution through the use of genomic © Jonesdown the & microorganisms Bartlett Learning, of infectious disease. LLC Pasteur’s ©technologies Jones & has Bartlett expanded our Learning, understanding LLC of micro NOTlab FORstudied SALEthe mechanisms OR DISTRIBUTION for infection and developed NOTorganism FOR relationships. SALE OR DISTRIBUTION

© Jones & BartlettLEARN ILearning,NG Obje cLLCtives © Jones & Bartlett Learning, LLC NOT FORAfter SALE understanding OR DISTRIBUTION the textbook reading, you should be capable NOTof FOR8. SALEIdentify severalOR DISTRIBUTION discoveries made in the laboratories of Pasteur writing a paragraph that includes the appropriate terms and pertinent and Koch. information to answer the objective. 9. Describe how viruses were discovered. 1. Identify the significant contributions made by Hooke and 10. Describe the contributions Winogradsky and Beijerinck made to Leeuwenhoek that foreshadowed the beginnings of microbiology. environmental microbiology. 2. Discuss spontaneous© ge Jonesneration &an dBartlett compare the Learning, experiments LLC11. Briefly describe the organisms© Jones or agents & found Bartlett in each ofLearning, the micro- LLC that led to its downfall.NOT FOR SALE OR DISTRIBUTION biology disciplines. NOT FOR SALE OR DISTRIBUTION 3. Assess the importance of the work carried out by Semmelweis and 12. Illustrate how microorganisms and viruses make good model by Snow that went against the miasma idea and established the systems. field of epidemiology. 13. Explain why Bacteria and Archaea are prokaryotic cells and all other 4. Explain how Jenner’s work differs from earlier practices for prevent- organisms are eukaryotic cells. ing infectious disease. 14. Define chemotherapy and explain why antibiotics were referred 5. Discuss© Jones Pasteur’s & earlyBartlett studies Learning,suggesting that LLC germs could cause to as© “magic Jones bullets.” & Bartlett Learning, LLC disease.NOT FOR SALE OR DISTRIBUTION 15. OutlineNOT the FORmajor challenges SALE ORfacing DISTRIBUTION microbiology today. 6. Describe how Lister’s surgical work and Pasteur’s studies of pébrine 16. Assess the importance of microbial ecology and microbial evolution further strengthened the germ theory of disease. to the current Golden Age of microbiology. 7. Judge the importance of (a) the germ theory of disease and (b) Koch’s postulates to the identification of microbes as agents © Jones & Bartlettof infectious Learning, disease. LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

05940_CH01_0001_5thPgs.indd 31 12/19/11 12:51 PM 32 chapter 1 Microbiology: Then and Now

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOTFor FOR STEPS SALE A–D, answersOR DISTRIBUTION to even-numbered questions and problemsNOT FORcan be SALEfound in OR Appendix DISTRIBUTION C on the Student Companion Website at http://microbiology.jbpub.com/bodysystems2e/. In addition, the site features eLearning, an online review area that provides quizzes and other tools to help you study for your class. You can also follow useful links for in-depth information, read more MicroFocus stories, or just find out the latest microbiology news. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Step A: Self-TestNOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Each of the following questions is designed to assess your ability to 9. What group of microbial agents would eventually be identified from remember or recall factual or conceptual knowledge related to this the work of Ivanowsky and Beijerinck? chapter. Read each question carefully, then select the one answer A. Viruses that best fits the question or statement. B. Fungi 1. Who was the© Jonesfirst person & to Bartlett see bacterial Learning, cells with the microscope? LLC C. Protists © Jones & Bartlett Learning, LLC A. Pasteur NOT FOR SALE OR DISTRIBUTION D. BacteriaNOT FOR SALE OR DISTRIBUTION B. Koch 10. What microbiological field was established by Winogradsky and C. Leeuwenhoek Beijerinck? Hooke D. A. Virology 2. What process was studied by Redi and Spallanzani? B. Microbial ecology A. Spontaneous generation C. Bacteriology © Jones B. &Fermen Bartletttation Learning, LLC © JonesD. Mycology & Bartlett Learning, LLC Variolation C. 11. What group of microorganisms has a variety of internal cell NOT FORD. Antisepsis SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION compartments and acts as decomposers? What is the name for the field of study established by Semmelweis 3. A. Bacteria and Snow in the mid 1800s? B. Viruses A. Immunology C. Archaea B. Bacteriology D. Fungi Virology C. © Jones & Bartlett Learning,12. LLCWhich one of the following organisms© Jones was NOT & a Bartlett model organism Learning, LLC D. Epidemiology related to the birth of molecular genetics? The process of _____ involvedNOT the inoculation FOR SALE of dried OR smallpox DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 4. A. Streptococcus scabs under the skin. B. Penicillium A. vaccination C. Escherichia B. antisepsis D. Neurospora variolation C. 13. Which group of microbial agents is eukaryotic? immunization D. © Jones & Bartlett Learning, LLC A. Bacteria© Jones & Bartlett Learning, LLC 5. The process of controlled heating, called _____, was used to keep NOT FOR SALE OR DISTRIBUTION B. Viruses NOT FOR SALE OR DISTRIBUTION wine from spoiling. C. Archaea A. curdling D. Algae B. fermentation 14. The term antibiotic was coined by _____ to refer to antimicrobial C. pasteurization substances naturally derived from _____. variolation D. A. Waksman; bacteria and fungi © Jones6. What & surgicalBartlett practice Learning, was established LLC by Lister? © JonesB. Domagk; & Bartlett other living Learning, organisms LLC A. Antisepsis C. Fleming; fungi and bacteria NOT FORB. Chem SALEotherapy OR DISTRIBUTION NOT D.FOR Ehrlich; SALE bacteri ORa DISTRIBUTION Variolation C. 15. Which one of the following is NOT considered an emerging infectious D. Sterilization disease? Which one of the following statements is not part of Koch’s 7. A. Polio postulates? B. Hantavirus pulmonary disease A. The microorganism must be© isolatedJones from & aBartlett dead animal Learning, and LLCC. Lyme disease © Jones & Bartlett Learning, LLC pure cultured. D. AIDS The microorganism and diseaseNOT can FOR be identified SALE from OR a DISTRIBUTION NOT FOR SALE OR DISTRIBUTION B. 16. A _____ is a mixture of _____ that form as a complex community. mixed culture. A. genome; genes The pure cultured organism is inoculated into a healthy, C. B. biofilm; microbes susceptible animal. C. biofilm; chemicals The same microorganism must be present in every case of the D. D. miasma; microbes disease.© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 8. Match the lab with the correct set of identified diseases. A. Pasteur:NOT tetan FORus and SALEtuberculosis OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION B. Koch: anthrax and rabies C. Koch: cholera and tuberculosis D. Pasteur: diphtheria and typhoid

05940_CH01_0001_5thPgs.indd 32 12/19/11 12:51 PM Step D: Questions for Thought and Discussion 33

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEStep OR B: DISTRIBUTIONReview NOT FOR SALE OR DISTRIBUTION 17. Construct a concept map for Microbial Agents using the follow- 19. _____ Pasteur proposed that “wine disease” was a souring of wine ing terms. caused by yeast cells. algae Bacteria protists 20. _____ Antisepsis is the use of chemical methods for disinfecting Archaea fungi viruses living surfaces. cyanobacteria ©micr Jonesoorganisms & Bartlett Learning, LLC21. _____ Separate bacterial© colonies Jones can be& observedBartlett in a brothLearning, culture. LLC decomposers NOTnucleated FOR cells SALE OR DISTRIBUTION22. _____ Semmelweis proposedNOT that FOR cholera SALE was a waterborne OR DISTRIBUTION disease. On completing your study of these pages, test your understanding of 23. _____ Some bacterial species can convert nitrogen gas (N2) into their contents by deciding whether the following statements are true ammonia (NH3). (T) or false (F). If the statement is false, substitute a word or phrase 24. _____ Fungi are eukaryotic microorganisms. for the underlined word or phrase to make the statement true. 25. _____ Koch proposed the germ theory. 18. _____© Jones Leeuwenhoek & Bartlett believed that Learning, animalcules aroseLLC spontaneously 26. _____© VaJonesriolation involved& Bartlett inoculating Learning, individuals with LLC smallpox scabs. NOTfrom FOR decaying SALE matter. OR DISTRIBUTION 27. _____NOT Mycology FOR is theSALE scientific OR study DISTRIBUTION of viruses.

© Jones & BartlettStep C: Learning, applicatio LLCns © Jones & Bartlett Learning, LLC NOT FOR28. SALEAs a microbiologist OR DISTRIBUTION in the 1940s, you are interested in discoveringNOT FOR29. SALEAs an environmental OR DISTRIBUTION microbiologist, you discover a new species new antibiotics that will kill bacterial pathogens. You have been of microbe. How could you determine if it has a prokaryotic or given a liquid sample of a chemical substance to test in order to eukaryotic cell structure? Suppose it has a eukaryotic structure. determine if it kills bacterial cells. Drawing on the culture tech- What information would be needed to determine if it is a member niques of Robert Koch, design an experiment that would allow you of the protista or fungi? to determine the killing© Jonesproperties &of theBartlett sample substance. Learning, LLC30. Louis Pasteur once stated:© Jones “In the field& Bartlett of observation, Learning, chance LLC NOT FOR SALE OR DISTRIBUTION favors only the preparedNOT mind.” FOR How does SALE this quote OR apply DISTRIBUTION to the work done by (a) Semmelweis, (b) Snow, and (c) Fleming?

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC StepNOT FORD: Que SALEstio ORns DISTRIBUTION for thought and discussNOTion FOR SALE OR DISTRIBUTION 31. Many people are fond of pinpointing events that alter the course of 36. Who would you select as the “first microbiologist?” (a) Leeuwenhoek, history. In your mind, which single event described in this chapter (b) Hooke, or (c) Pasteur and Koch. Support your decision. had the greatest influence on the development of microbiology? 37. Felix Pouchet was a French biologist and science writer who believed What event would be in second place? in spontaneous generation. As such, he was often in debate with © Jones &32. BartlettOne of the Learning,foundations of scientificLLC inquiry is proper experimental© Jones &Pasteur Bartlett because Learning, he was not convincedLLC that Pasteur’s experiments NOT FOR SALEdesign OR involving DISTRIBUTION the use of controls. What is the role of a controlNOT FOR SALErefuted the OR idea DISTRIBUTION of spontaneous generation. As proof, Pouchet set in an experiment? For each of the experiments described in the up a series of swan-necked flasks identical to those used by Pasteur section on spontaneous generation, identify the control(s) and to refute spontaneous generation. He then filled the flasks with a explain how the interpretation of the experimental results would broth made from hay, boiled the flasks for one hour, and allowed change without such controls. them to cool. Everything was identical to Pasteur’s experiments 33. One reason for the rapid advance in knowledge concerning molecular except Pasteur used a sugar and yeast extract broth and only boiled biology during the second© Jones Golden Age & ofBartlett microbiology Learning, was because LLC the flasks for a few minutes.© Jones & Bartlett Learning, LLC many researchers usedNOT microorganisms FOR SALE as model ORsystems. DISTRIBUTION Why would In all cases, PouchetNOT saw growth FOR of SALE microorganisms OR DISTRIBUTION in all his bacterial cells be more advantageous to use for research than, say, flasks, even with boiling for one hour. Propose a solution for the rats or guinea pigs? contradictory results of Pasteur and Pouchet, knowing that (a) what 34. When you tell a friend that you are taking microbiology this semester, both scientists saw was valid and correct, and (b) spontaneous generation does not occur. she asks, “Exactly what is microbiology?” How do you answer her? If you remain stumped, check out the short paper entitled: John 35. As microbiologists continue to explore the microbial universe, it is © Jones & Bartlett Learning, LLC Tyndall© Jones and the Spontaneous& Bartlett Generation Learning, Debate LLC (Microbiology bNOTecoming FOR more apparentSALE that OR microbes DISTRIBUTION are “invisible emperors” that TodayNOT, No vemberFOR 2005-http:www.sgm.ac.uk/pubs/micro_today/SALE OR DISTRIBUTION rule the world. Now that you have completed Chapter 1, provide pdf/110501.pdf examples to support the statement: Microbes Rule!

05940_CH01_0001_5thPgs.indd 33 12/19/11 12:51 PM