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© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC The MicrobialNOT FOR SALE OR DISTRIBUTION World: NOT FOR SALE OR DISTRIBUTION Surprising and Stunning 1 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Looking Ahead Perhaps you’ve heard the saying “there are more stars in the heavens than We share our world with thousands of species of plants and animals that we can see and thou- all the grains of sand on © Jones &sands Bartlett of species Learning, of microbes LLC that we cannot see. This© microbial Jones world& Bartlett is both Learning, surprising and LLCEarth.” The same may be stunning—surprising because it contains such a wealth of different forms of life, and stunning said of microbes and NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONgrains of soil. Without because we scarcely understand how those life forms affect our own world. This chapter begins microbes to, for example, our trek into the microbial world with some insights into an invisible realm. take nitrogen from the air On completing this chapter, you should be able to . . . and transfer it to the soil • appreciate how the microbial world affects our world in such areas as agriculture, where it is essential for plant growth, we would industry, research,© Jones and the & environment; Bartlett Learning, LLC © Jonesnever & Bartlett see the diversity Learning, of LLC • provide numerousNOT examples FOR SALE of how OR microbes DISTRIBUTION contribute substantially to the qualityNOT FORplant SALE life we do,OR such DISTRIBUTION as of our lives; in this colorful tulip field. • discuss the origins of microbiology and how these origins are related to studies on spontaneous generation; •© describeJones &the Bartlett contributions Learning, of Louis LLC Pasteur and Robert Koch to© theJones development & Bartlett of Learning, LLC NOTthe scienceFOR SALE of microbiology; OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION • provide thumbnail sketches of bacteria, viruses, protozoa, and other members of the microbial world; and • understand the diversity of microbes and explain why an appreciation of micro- © Jones & Bartlettbiology Learning, encourages LLC an appreciation of life. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 5

6 CHAPTER 1 The Microbial World: Surprising and Stunning Each year, a group of pilgrims gather in the English countryside outside the vil- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLClage of Eyam and pay homage to the townsfolk who three and a half centuries before NOT FOR SALE OR DISTRIBUTIONgave their lives so that othersNOT might FOR live.SALE The OR pilgrims DISTRIBUTION bow their heads and remem- ber what happened that fateful year. Bubonic plague had erupted in Eyam during the spring of 1665, and before long, many had fled to the countryside. But most of the townsfolk realized that by doing © Jonesso they & Bartlett would probably Learning, spread LLC the plague to nearby communities.© Jones &They Bartlett were con- Learning, LLC NOT FORfronted SALE not only OR byDISTRIBUTION the terrible disease but also by the NOTmoral FORdilemma SALE they OR faced. DISTRIBUTION Then the village rector made a passionate plea that the remainder of the townsfolk stay, and after much soul-searching, they reluctantly decided to do so and take their chances. They marked off the village limits with a circle of stones, and the neighbor- ing villagers brought food and other supplies to the self-quarantined group. In the © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC end, 259 of Eyam’s 350 people died of the plague. NOT FOR SALE OR DISTRIBUTIONThe memorial service has a poignant momentNOT FOR as the SALE pilgrims OR join DISTRIBUTION their hands and somberly recite a poem whose roots trace to that period: Ring-a-ring of rosies © Jones & Bartlett Learning, LLC A pocketful of posies© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION Achoo! Achoo! NOT FOR SALE OR DISTRIBUTION We all fall down. There is no laughter in the group; indeed, some are moved to tears. The ring of rosies refers to the rose-shaped splotches that surrounded the neck and shoulders of © Jonesplague & Bartlett victims. Posies Learning, were flowers LLC that people tucked into© Jones their pockets & Bartlett hoping Learning, to LLC NOT FORward offSALE the evil OR spirits. DISTRIBUTION “Achoo” refers to the fits of sneezingNOT that FOR accompany SALE plague;OR DISTRIBUTION and the last line, the saddest of all, refers to the death that claimed so many plague victims. Disease has always left people thunderstruck with terror. Before the late 1800s, however, that fear was compounded by ignorance because no one was really sure what causes © Jones & Bartlett disease,Learning, much LLC less how to deal with it. As ©we Jones shall see & later Bartlett in this chapter,Learning, the answers LLC NOT FOR SALE ORwould DISTRIBUTION not start coming until the late 1800s,NOT when FOR Louis SALE Pasteur ORand RobertDISTRIBUTION Koch solid- ified the link between infectious disease and microscopic forms of life. These life forms Bacteria The domain of living include bacteria, viruses, fungi, protozoa, and other groups of organisms invisible to things that includes all the unaided eye. Many scientists refer to them as “microorganisms,” but we shall use organisms not classified as microbes © JonesArchaea & Bartlettor Eukarya. Learning, LLCthe equally acceptable and© moreJones simplified & Bartlett term “Learning,.” This LLC term was coined in 1879 by the French scientist Charles E. Sedillot. It implies any living thing that must NOT FORvirus SALEAn infectious OR DISTRIBUTIONagent NOT FOR SALE OR DISTRIBUTION consisting of DNA or RNA and be magnified to be seen. surrounded by a protein sheath; To be sure, most of us are inclined to think of disease when we think of microbes. in some cases, a membranous And this connection is probably justified because some microbes cause much misery envelope surrounds the coat. and pain. But microbes are also responsible for much that adds quality to our lives. Fungi One of the five kingdoms© JonesFor &instance, Bartlett microbes Learning, break LLCdown the remains of everything© Jones that dies& Bartlett and recycle Learning, LLC in the Whittaker classification of living organisms; composed NOTof FORthe essential SALE elementsOR DISTRIBUTION so that vital nutrients can be regenerated.NOT FOR Moreover, SALE the OR very DISTRIBUTION the molds and yeasts. air we breathe is a product of microbial chemistry because certain microbes perform protozoan (pl. protozoa) A photosynthesis (the process by which light energy is converted into chemical energy) single-celled eukaryotic organism in the vast expanses of the forests and oceans, where they generate the oxygen that that lacks a cell wall and usually sustains us. Closer to home, many species of microbes live in our mouth, skin, intes- exhibits ©chemoheterotrophic Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC tines, respiratory tract, and other body systems, where they prevent the multipli- metabolism.NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION microbe (microorganism) A cation of organisms that might cause disease. Microbes are also responsible for the microscopic form of life final forms of many foods we eat, including fermented dairy products such as yogurt, including bacterial, archaeal, buttermilk, and sour cream. We shall embellish on these and other ways in which fungal, and protozoal cells. microbes influence humans and society as we begin our journey through the micro- © Jones & Bartlett Learning, LLCbial world. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Why Microbes Matter 7

© Jones & BartlettWhy Microbes Learning, Matter LLC © Jones & Bartlett Learning, LLC NOT FORIf SALEyou took OR a pinch DISTRIBUTION of rich soil and placed it in the palmNOT of your FOR hand, SALE you would OR DISTRIBUTION come face-to-face with an estimated billion microbes—bacteria, viruses, fungi, protozoa, and numerous other microscopic forms of life, shown in FIGURE 1.1 . To appreciate the extraordinarily small size of the microbes, consider this: If you were to count the microbes in a pinch of© soil Jones at a rate & Bartlettof one per Learning, second without LLC stopping, it would take © Jones & Bartlett Learning, LLC over 33 years to completeNOT your FOR counting. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION But we are not here to count microbes. Rather, we are here to appreciate them, and so we should ask: What are the microbes doing in the soil, and why are they there? To be sure, some are disease-causing (pathogenic) microbes, probably in transit from one living thing to another. Others, however, are probably quite benign. By their sheer numbers, ©they Jones control & the Bartlett pathogens Learning, in the soil andLLC maintain nature’s balance© in Jones the environ- & Bartlett Learning, LLC ment.NOT Many FOR species SALE capture OR energy DISTRIBUTION from the sun and store that energyNOT in the FOR form SALEof OR DISTRIBUTION sugar molecules; to do this, they use the chemistry of photosynthesis, the same chemistry that adds oxygen to our atmosphere. Other species are decomposers, the great recy- clers of nature that return carbon, nitrogen, sulfur, and other elements to the atmosphere © Jones &so Bartlettthat they can Learning, be used to LLCrenew the chemical molecules© Jonesessential &to Bartlettlife’s continuance. Learning, LLC NOT FOR SALEAnd theseOR DISTRIBUTION are but a few of the ways that microbesNOT benefit FOR society. SALE Some OR DISTRIBUTIONother examples are presented in the following paragraphs.

Down on the Farm A cow rests peacefully under a tree on a sunlit day in an open meadow and chews its cud. The scene is calm© andJones reassuring & Bartlett and makes Learning, us feel thatLLC all is well in the world © Jones & Bartlett Learning, LLC (FIGURE 1.2 ). We mightNOT even FOR be SALEinclined OR to thinkDISTRIBUTION of Beethoven’s beautiful Sixth NOT FOR SALE OR DISTRIBUTION Symphony—The Pastorale—with its endless visions of the charm and grace of the countryside.

Viruses Multicellular algae

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

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

Fungi

Cyanobacteria FIGURE 1.1 A Microbial Menagerie. A menagerie of microbes as conceived by an artist. Most of these organisms and many others are present in a pinch of rich soil. All are discussed in later chapters © Jones &of thisBartlett book. Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

8 CHAPTER 1 The Microbial World: Surprising and Stunning

FIGURE 1.2 Microbial Factories. These cows lazily enjoying the afternoon sun are in fact microbial factories. Within the cow’s first stomach (the rumen), various species of microbes are breaking down grasses and plants and assisting the conversion of carbohydrates to proteins of the cow’s muscle and dairy prod- © Jonesucts. &The Bartlett cow chews theLearning, regurgitated LLCmass, the cud, to help the microbes© make Jones the essential & Bartlett conversions. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

But in the gut of the cow, microbes are busily at work. They have mixed with grasses in the first stomach of the cow (the rumen) and have begun the conversion of carbohydrate to protein, a conversion that will turn parts of the plants the cow eats © Jones & Bartlett intoLearning, its muscle LLC and dairy products. Soon© the Jones cow will & Bartlettregurgitate Learning, the material LLC from NOT FOR SALE ORthe DISTRIBUTION rumen, chew it a bit to mix in some saliva,NOT FORthen reswallow SALE OR the DISTRIBUTION mixture for more fermentation A metabolic fermentation. At the end of the line, we can expect hamburgers and dairy products, pathway in which carbohydrates as we explore further in Chapter 15. serve as electron donors, the final electron acceptor is not In other areas of agriculture, humans use microbes as insecticides and pesticides. © Jonesoxygen & Bartlett gas (O2), andLearning, NADH is LLCOne bacterium called Bacillus© Jones thuringiensis & Bartlettis sprayed Learning, onto plants, LLC where its poisonous reoxidized to NAD+ for reuse in toxins kill the caterpillar forms of many agricultural pests. Biotechnologists have even NOT FORglycolysis SALE for generationOR DISTRIBUTION of ATP; NOT FOR SALE OR DISTRIBUTION see also industrial fermentation. extracted from these bacteria the genes that encode their toxins and biochemically inserted those genes into plant cells. Remarkably, the plants then produce the insecti- B. thuringiensis B. thur-in-je¯-en′sis cidal toxins as they grow in the field. Most of the soybean plants currently in American fields contain these bacterial genes. And this astounding accomplishment is only the © Jonesbeginning & Bartlett of what Learning, promises to LLC be an agricultural revolution© inJones the decades & Bartlett ahead. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION In the Industrial Plant On an industrial scale, microbes are cultivated in huge batches in building-sized tanks, where they produce chemicals such as lactic, acetic, and other organic acids, as well © Jones & Bartlett asLearning, the amino LLCacids used to construct proteins.© Jones The citric& Bartlett acid in Learning,a bottle of soda, LLC for example, is produced by fungi. And bacterial proteins produced in industrial quan- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION tities are used in laundry detergents, as well as in adhesives and in baking, as we explore in Chapter 14. In our foods, microbial proteins are used to tenderize meat, to clarify fruit juices, and to soften the centers of chocolate-covered cherries. Working like miniature chemical factories, the microbes churn out industrial quantities of vita- © Jones & Bartlett Learning, LLCmins (especially B vitamins)© Jones that eventually & Bartlett find Learning,their way into LLC the tablets we take to NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Why Microbes Matter 9 promote good health. Even some perfumes contain products of microbial origin— © Jones & Bartlett Learning, LLC © Jones musk& Bartlett oil, for Learning, instance, is theLLC product of the chemistry in a fungus. NOT FOR SALEAlthough OR mostDISTRIBUTION natural food flavorings are producedNOT from FOR plants SALE by ORtraditional DISTRIBUTION processes, new industrial methods have made it possible to use microbes to convert relatively cheap starting materials into higher-value flavor and aroma additives. These additives are then used in foods and beverages as well as in cosmetics and other con- sumer items. Examples© areJones the peach & Bartlett and coconut Learning, flavoring agentsLLC belonging to a chem- © Jones & Bartlett Learning, LLC ical group called lactones.NOT AlthoughFOR SALE lactones OR can DISTRIBUTION be generated from the fats in sweet NOT FOR SALE OR DISTRIBUTION potatoes, these fats are expensive to modify and occur only in low concentrations in the potatoes. To circumvent these problems, microbiologists use fungi to convert less expensive and more available fats into compounds that other microbes can easily transform to lactones. Transitions like these were studied a century ago by one of the first © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC industrial microbiologists, whose life is explored in A Closer Look below. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION At the Hub of Biotechnology Perhaps the most sophisticated contemporary use of microbes is in biotechnology. In biotechnology The commercial this industry, various species of bacteria and yeasts are used as living factories to pro- application of genetic engineering using living © Jones &duce Bartlett such products Learning, as insulin LLC for diabetics, blood-clotting© Jones Factor & VIII Bartlett for hemophil- Learning, organisms.LLC NOT FORiacs, SALE and ORhuman DISTRIBUTION growth hormone for undersized individuals.NOT FOR Microbes, SALE OR especially DISTRIBUTION viruses, are also used to ferry genes into tissue cells during gene therapy, as we note later in this chapter. Other viruses have been genetically altered to increase disease resistance in plants and to kill insect pests in the environment, as Chapter 16 explains. And some yeasts have been modified to produce viral proteins that can be used in vaccines, such as the© one Jones for hepatitis & Bartlett B. Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

A CLOSER LOOK Of Microbes and Cherry Trees

During© Jones the 1880s, & Bartlett while medical Learning, microbiologists LLC were searching out the causes© Jones of & Bartlett Learning, LLC infectiousNOT FOR disease, SALE a Japanese OR DISTRIBUTIONbiochemist was busy acquiring enormous experienceNOT FOR and SALE OR DISTRIBUTION wealth as one of the first industrial microbiologists. His name was Jokichi Takamine. In the 1870s, Takamine left his native Japan to study engineering in the West. By the 1890s, he had married an American and was an expert on the enzymes of a com- . mon mold named Aspergillus (a-sper-jil′lus). In one of his first successes, Takamine iso- © Jones & Bartlettlated and purified Learning, an Aspergillus LLC enzyme, and he used it© to Joneshelp make & whiskey Bartlett at his Learning, LLC NOT FOR SALEfermentation OR DISTRIBUTION plant in Peoria, Illinois. Local brewers turnedNOT against FOR his SALE innovative OR DISTRIBUTION methods, however, so he patented the enzyme and licensed it to a pharmaceutical company. The company mixed it with peppermint and sold it as a digestive aid. Marketed as “takadiastase,” the enzyme became the Alka-Seltzer of the 1890s. Takamine next moved to New York, where he and an assistant set out to isolate the active principle (the ©hormone) Jones in & adrenal Bartlett glands. Learning, For months, LLC they separated, precipi- © Jones & Bartlett Learning, LLC tated, dissolved, purified,NOT and FOR repurified SALE in ORtheir DISTRIBUTION hunt for the elusive substance. Then NOT FOR SALE OR DISTRIBUTION one night, his assistant, too tired to wash the glassware, left it by the sink and went home. The next day, a glass containing extracts from adrenal gland tissue was lined with crystals of epinephrine (adrenaline). The isolation was a success. Takamine’s patent rights to epinephrine yielded wealth beyond his imagination. ©In Jones later years, & BartlettTakamine became Learning, a patron LLC of the arts and a philanthropist.© JonesOn August & Bartlett Learning, LLC 30,NOT 1909, FOR the city SALE of Tokyo OR announced DISTRIBUTION a gift to the people of the United NOTStates: FORThe SALE OR DISTRIBUTION city would be honored to adorn the Tidal Basin in Washington, D.C. with dozens of Japanese cherry trees. In the decades that followed, the cherry trees grew to become a splendid attraction in the nation’s capital and an annual harbinger of spring. What few people know is that the gift was funded anonymously by Jokichi Takamine. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

10 CHAPTER 1 The Microbial World: Surprising and Stunning

© Jones & Bartlett Learning, LLC There is even a bacterial© Jonescement that& Bartlett researchers Learning, have used toLLC fix cracks in concrete NOT FOR SALE OR DISTRIBUTIONblocks. Biochemists beginNOT with FOR species SALE of bacteria OR DISTRIBUTION that digest a nitrogen-containing compound called urea (the major waste product of urine). They mix the bacteria with sand, calcium chloride, and urea. When the bacteria break down the urea, they produce carbon dioxide and ammonia, which reacts with water to form ammonium hydroxide. © JonesThe & latter Bartlett reacts withLearning, the carbon LLC dioxide and the calcium chloride© Jones to produce& Bartlett calcium Learning, LLC NOT FORcarbonate, SALE which OR crystallizesDISTRIBUTION to form limestone and fill theNOT cracks FOR in the SALE concrete. OR One DISTRIBUTION observer has whimsically suggested that science has finally found a “concrete use for bacteria.”

With Most Meals © Jones & Bartlett RarelyLearning, does a mealLLC go by when we do not rely© Jones on microbes & Bartlett for something Learning, on our LLC plate NOT FOR SALE ORor DISTRIBUTION in our glass (as FIGURE 1.3 illustrates). Sausages,NOT FOR for SALE example, OR owe DISTRIBUTION their tangy taste to microbial activity. The food industry also depends on microbes to produce sauer- kraut, pickles, and vinegar. Many dairy products and cheeses result from microbial action on milk. Virtually all types of bread depend on microbes for their taste and spongy textures. The wine and beer at the hub of the fermentation industries could © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC not be produced without microbes. Even the coffee we drink depends in part on NOT FOR SALE OR DISTRIBUTIONmicrobes for its flavor andNOT aroma. FOR Chapter SALE 12 OR explores DISTRIBUTION these and other fascinating uses for microbes in food production. On the negative side, foods are among the principal vehicles for transporting pathogenic microbes among individuals. Chicken, eggs, and other poultry products, for Salmonella © Jonesexample, & Bartlett are notorious Learning, for their LLC populations of Salmonella©, whichJones can & infectBartlett individ- Learning, LLC säl-mo¯n-el′lä NOT FORuals who SALE fail ORto cook DISTRIBUTION these foods properly. In some cases,NOT individuals FOR SALE unknowingly OR DISTRIBUTION contaminate uncooked foods. For example, they use a knife to cut up raw chicken and then, without washing it, use the same knife to cut up salad fixings. Scientists are working to resolve the Salmonella problem, as A Closer Look on page 11 points out. In the meantime, public health officials advise thorough cooking of poultry products. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

FIGURE 1.3 An Array of Foods and Beverages Produced by Microbes. Society is dependent on © Jones & Bartlett Learning, LLCmicrobes for many of its foods.© Fermented Jones foods & Bartlett and dairy products Learning, are examples. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Why Microbes Matter 11

In the old days, chicks hatched from their eggs, scrambled to their feet, and nestled under their mother’s wing until it was safe to come out. By staying close to their mother hen, the chicks received protection, caring . . . and bacteria. Bacteria? Yes, bacteria—hundreds ©of strainsJones of &harmless Bartlett organisms Learning, that entered LLC the chicks’ guts and © Jones & Bartlett Learning, LLC prevented SalmonellaNOTspecies FOR from SALE causing ORinfection. DISTRIBUTION With all the harmless entero- NOT FOR SALE OR DISTRIBUTION cocci, lactobacilli, and other strains of bacteria lurking about, there simply was no room for Salmonella. The chicks remained healthy. But mother hen is gone. The high-tech chicken farms of today use machines to remove the eggs from the hens as they are produced. The chicks hatch and develop without© Jones ever seeing & Bartlett what made Learning, them. To be LLC sure, that is sad, but microbiologically© Jones & Bartlett Learning, LLC speaking,NOT FOR the sadness SALE is compoundedOR DISTRIBUTION by the absence of the harmless bacteriaNOT from FOR the SALE OR DISTRIBUTION chick’s gut. This absence encourages the chicks to acquire and develop Salmonella infection. And when they become fully grown chickens, they pass the Salmonella on to humans, where it causes severe intestinal disease. As of 1998, there was an answer. That year, the Food and Drug Administration approved © Jones & Bartletta spray called Learning, Preempt that LLC showers chicks with a mix of 29© speciesJones of &harmless Bartlett bacteria. Learning, LLC NOT FOR SALEThe chicks OR pick DISTRIBUTION the bacteria off their feathers and swallowNOT them. FORAs the harmlessSALE bacteriaOR DISTRIBUTION set up housekeeping in a chick’s gut, they compete with and exclude the dangerous ones. (Scientists call the process “competitive exclusion.”) Numerous research experiments show that the harmless bacteria crowd out the Salmonella species and significantly reduce or completely eliminate them. Once again, science has replaced mother hen. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

And when preparing eggs, the operative expression from health agencies is “Scramble or gamble.” © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC In theNOT Environment FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Although many people think of microbes as water pollutants, the more modern view is that microbes can be effectively used to alleviate pollution. This immensely appeal- ing way of putting microbes to work for society is called bioremediation. When an oil bioremediation The use of spill occurs, for instance, technologists add nitrogen, phosphorus, and other mineral microorganisms to degrade toxic © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, wastesLLC and other synthetic nutrients to the water and encourage microbes to grow and gorge themselves on the NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONproducts of industrial pollution. petroleum (as Chapter 16 details). Oil in areas treated this way clears away faster than that in areas not treated. Bioremediation is also used to eliminate other environmental pollutants, such as the waste products of explosives, as well as cleaning agents and radioactive compounds. Additionally, microbes© Jones remain & Bartlett the prime Learning, factor in sewage LLC treatment. In some © Jones & Bartlett Learning, LLC municipalities, wasteNOT is piped FOR into SALE oxidation OR DISTRIBUTION lagoons, where microbes digest the NOT FOR SALE OR DISTRIBUTION organic matter and completely convert the complex compounds into simple ones that can be recycled. In larger cities, waste treatment plants rely on microbial chemistry to handle the massive amounts of sewage and garbage generated daily. Various stages of treatment© Jones address & Bartlett various Learning, types of waste, LLC and soon the ugly profusion© Jones of grime, & Bartlett Learning, LLC gunk,NOT and grotFOR is SALEconverted OR to DISTRIBUTION chemical fertilizers that can be used asNOT soil enhancers FOR SALE OR DISTRIBUTION for growing crops.

In the Pharmaceutical Lab Most microbiologists are dreamers, and those who work in pharmaceutical laborato- © Jones &ries Bartlett are among Learning, the more imaginative LLC ones. These individuals© Jones continue & Bartlett the search Learning, for LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

12 CHAPTER 1 The Microbial World: Surprising and Stunning new medicines to combat the emerging diseases of our era. For example, when a cer- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC tain author was growing up in the Bronx, doctors had not yet heard of Lyme disease, NOT FOR SALE OR DISTRIBUTIONLegionnaires’ disease, or AIDS.NOT In FOR today’s SALE world, OR each DISTRIBUTION of these diseases is a serious health problem, and pharmaceutical scientists are hard at work searching for effective treat- ments and vaccines. They try modifications of existing drugs while exploring new approaches for innovative therapies, as we study in Chapter 15. © Jones &And Bartlett the approaches Learning, they useLLC often boggle the imagination.© Jones For example, & Bartlett it is now Learning, LLC NOT FORpossible SALE to extract OR DISTRIBUTION the genes from the virus that causes genitalNOT herpes FOR and SALE insert OR those DISTRIBUTION genes into cells isolated from the human immune system. Using the new genes in conjunction with their own genes, the cells then synthesize antibodies, a series of highly specific proteins that bind to and destroy the herpes virus in the body. But there antibody©A Joneshighly specific & Bartlett isLearning, more: Biotechnologists LLC can also obtain© from Jones the cells & Bartlett the complete Learning, set of antibody LLC protein produced by the body in genes and transfer them to soybean plants. Sown in the fields, the soybean plants pro- responseNOT to a foreign FOR substance, SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION such as a bacterium or virus, and duce antiherpes antibodies. (Scientists whimsically refer to these antibodies as “plan- capable of binding to the tibodies.”) Indeed, it may some day be possible to fight genital herpes merely by eating substance. a soybean product. New diagnostic tests are also in the future. Pharmaceutical scientists (FIGURE 1.4 ) © Jonesgene & probeBartlettA short Learning, piece of LLCare now producing gene ©probes Jones, collections & Bartlett of small Learning, fragments LLC of deoxyribonucleic NOT FORsingle SALE stranded OR DNA DISTRIBUTION which is acid (DNA), the materialNOT of which FOR genes SALE are ORmade. DISTRIBUTION Gene probes seek out and unite radioactively labeled that will hybridize with or bind to a with the complementary DNA of a microbe much like a left hand meets its comple- complementary target DNA or mentary right hand when one claps. Once the match is made, a biochemical signal is RNA strand. sent, and the technologist knows that a specific microbe is present. This remarkable © Jonestechnology & Bartlett even makesLearning, it possible LLC to diagnose a disease without© Jones cultivating & Bartlett the respon- Learning, LLC NOT FORsible pathogen.SALE OR And DISTRIBUTION the probes can also be used to find the NOTDNA fingerprintFOR SALE of a ORmicro- DISTRIBUTION bial contaminant (rather than the microbe itself) in an environmental sample. The explosive developments in pharmaceutical microbiology are paralleled by equally explosive research in other arenas. For example, scientists are exploring the

FIGURE 1.4 The Research Lab. Scientists continue to use microbes as centerpieces of their research © Jones & Bartlett Learning, LLCto develop imaginative and novel© Jonespharmaceutical & Bartlett products. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Roots of Microbiology 13 hydrothermal vents at the bottoms of the oceans and identifying strange and unusual © Jones & Bartlett Learning, LLC © Jones microbes;& Bartlett they Learning, are looking forLLC evidence of life on Mars by determining whether microbes NOT FORcould SALE survive OR conditionsDISTRIBUTION on that planet; they are discoveringNOT FOR new SALE clues to OR evolution DISTRIBUTION by studying the DNA of microbial forms that have been in existence for eons; and they are developing new concepts of the richness of life on Earth by focusing on microbial diversity. To be sure, it is a wonderful time to be studying microbiology. However, we must© pauseJones before & Bartlett we get too Learning, deeply into LLC the study of microbes, for, © Jones & Bartlett Learning, LLC as one philosopher hasNOT said, FOR to understand SALE OR where DISTRIBUTION you are going, you must know where NOT FOR SALE OR DISTRIBUTION you have been. And so, before we launch into our study of microbiology, we shall sur- vey its origins; for our roots give us the strength to grow upward and outward.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC TheNOT Roots FOR SALE of Microbiology OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Robert Hooke The microbial world was virtually unknown until the mid-1600s, when an English scientist named Robert Hooke became fascinated with a newly developed instrument, © Jones &the Bartlett microscope, Learning, and wrote LLC about his observations. Although© Jones Hooke & Bartlett is best remem-Learning, LLC NOT FORbered SALE for ORhis descriptions DISTRIBUTION of minute compartments inNOT slices FORof cork SALE (which OR he named DISTRIBUTION “cells”), he also reported the microscopic details of threadlike fungi, referring to them as “elongated stalks.” Hooke’s curiosity led him to study the fungus that infects rose plants, and his illustrations of its threads were among the first descriptions of a microbe. But Hooke could scarcely© Jones imagine & Bartlettwhat others Learning, would find LLC in this invisible world. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Anton van Leeuwenhoek The individual best remembered for bringing microbes to the world’s attention is a Dutch merchant named Anton van Leeuwenhoek, pictured in FIGURE 1.5a . In the 1670s, van Leeuwenhoek Leeuwenhoek developed the skill of grinding lenses for the purpose of magnifying and lay′wen-hoke © 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,Screw LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONplate

Elevating © Jones & Bartlett Learning, LLC © Jones &s crewBartlett Learning, LLC (a) NOT FOR SALE OR DISTRIBUTION NOT FOR(b) SALE OR DISTRIBUTION FIGURE 1.5 Anton van Leeuwenhoek. (a) Van Leeuwenhoek at work in his study. Using a primitive microscope, van Leeuwenhoek was able to achieve magnifications of over 200 times and describe various biological specimens, including numerous types of microbes. (b) Details of van Leeuwenhoek’s lens system. The object is placed on the point of the specimen mount. The mount is adjusted by turning the focusing screw and the elevating screw. Light is reflected from the specimen through the lens, thereby © Jones &magnifying Bartlett the Learning,specimen. LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

14 CHAPTER 1 The Microbial World: Surprising and Stunning inspecting cloth. Soon he was using the lenses to satisfy his own curiosity. Squinting © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLCthrough a lens, van Leeuwenhoek studied the eye of an insect, the scales of a frog’s skin, NOT FOR SALE OR DISTRIBUTIONand the intricate details of NOTmuscle FOR cells. SALEIn 1673, OR while DISTRIBUTION peering into a drop of pond water, he came upon microscopic forms of life, darting back and forth and rolling and tumbling in this microcosm of life. He dubbed the microbes “animalcules” (he assumed they were tiny animals). They at first delighted him, then amazed him with their variety, and finally © Jonesperplexed & Bartlett him as Learning, he pondered LLCtheir meaning. Today, we recognize© Jones that & the Bartlett microbes Learning, he LLC NOT FORsaw were SALE protozoa. OR DISTRIBUTION To the best of our knowledge, few had NOTseen them FOR before. SALE OR DISTRIBUTION Van Leeuwenhoek excitedly communicated his findings to a group of English scientists called the Royal Society. The members of the society encouraged van Leeuwenhoek to continue his work, and over the next 40 years, he wrote a long series of letters describing the new microscopic forms he observed. His letter of September © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 17, 1683 is particularly noteworthy because it apparently contains the first known NOT FOR SALE ORdescriptions DISTRIBUTION of bacteria. In other letters, heNOT described FOR spermSALE cells OR and DISTRIBUTION drew represen- tations of microscopic yeast cells he gathered from the bottom of a beer vat. Van Leeuwenhoek became one of the most famous individuals of his time, and he hosted royalty and heads of state, who came to peer into his lenses. When he died in 1723, © Jones & Bartlett Learning, LLChe was 90 years old, in itself© Jones an achievement & Bartlett for Learning,those times. LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Louis Pasteur After the passing of van Leeuwenhoek, interest in microbes gradually waned for at least two reasons: Scientists lacked the technology for learning about microbes; and most people believed that microbes were mere curiosities with little or no effect on © Jonessociety. & Bartlett In the 1850s, Learning, however, LLC both of these reasons changed© Jones with the & workBartlett of Louis Learning, LLC NOT FORPasteur SALE and his OR contemporaries. DISTRIBUTION Pasteur, the renowned FrenchNOT scientist,FOR SALE called OR atten- DISTRIBUTION tion to the microbes as possible agents of infectious disease. When he was proven cor- rect, the technology for studying microbes rapidly developed. Pasteur, shown in FIGURE 1.6 , believed that the discoveries of science should have © Jones & Bartlett practicalLearning, applications, LLC and in 1857, he seized© Jones the opportunity & Bartlett to Learning,try and unravel LLC the NOT FOR SALE ORmystery DISTRIBUTION of why French wines were turningNOT sour. FOR The SALEprevailing OR theory DISTRIBUTION held that fer-

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (a) (b) FIGURE 1.6 Louis Pasteur. Two portraits of Louis Pasteur, one of the founders of the science of microbiology. (a) As a young man while studying chemistry at the École Normale Supèrieure. (b) As a scientist working in a laboratory in his home. In his right hand, Pasteur holds a flask of broth previously exposed to microbes in the air and now cloudy with growth. In his left hand, he is holding a © Jones & Bartlettswan-neck Learning,flask, in which theLLC broth is clear because airborne© microscopic Jones &organisms Bartlett could Learning, not enter through LLC the neck of the flask. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Roots of Microbiology 15 mentation results from the purely chemical breakdown of grape juice to alcohol. No © Jones & Bartlett Learning, LLC © Jones living& Bartlett thing seemedLearning, to be LLC involved. But Pasteur’s microscope consistently revealed NOT FORthat SALE wine ORcontained DISTRIBUTION large numbers of tiny microbes knownNOT FOR as yeast SALE cells. OR Moreover, DISTRIBUTION he noticed that sour wines contained populations of the barely visible bacteria described by van Leeuwenhoek. In a classic series of experiments, Pasteur boiled several flasks of grape juice and removed all traces of yeast cells from the flasks; he then set the juice aside to see if it© would Jones ferment. & Bartlett Nothing Learning, happened. LLC Next, he carefully added © Jones & Bartlett Learning, LLC pure yeast cells back NOTinto the FOR flasks, SALE and soonOR DISTRIBUTIONthe fermentation was proceeding nor- NOT FOR SALE OR DISTRIBUTION mally. Moreover, he found that if he used heat to remove all bacteria from the grape juice, the wine would not turn sour; it would not “get sick.” Pasteur’s work shook the scientific community because it showed that microscopic yeast cells and bacteria are tiny, living factories where important chemical changes take © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC place; indeed, scientists began to wonder if bacteria could also make people sick. In 1857,NOT Pasteur FOR published SALE a ORshort DISTRIBUTION paper on the bacterial souring of milk,NOT and he FOR implied SALE OR DISTRIBUTION that microbes might be related to human illness. In so doing, he set down the founda- tion for the germ theory of disease, a fundamental tenet holding that microbes play sig- germ theory of disease The nificant roles in the development of infectious disease. Pasteur also recommended principle formulated by Pasteur and proved by Koch that © Jones &using Bartlett heat to Learning, control bacterial LLC contamination. Acceptance© Jones of his technique,& Bartlett known Learning, as microorganismsLLC are responsible NOT FORpasteurization, SALE OR DISTRIBUTION eventually ended the sour wine problemNOT and FOR made SALE Pasteur OR famous. DISTRIBUTIONfor infectious diseases. Pasteur’s interest in microbes grew as he learned more about them. He found bacteria in soil, water, and air, and, importantly, in the blood of disease victims. He rea- soned that microbes might enter the blood from the environment; if so, perhaps they could be killed in the© environment Jones & Bartlettand their spreadLearning, halted. LLC However, many other sci- © Jones & Bartlett Learning, LLC entists had a differentNOT opinion: FOR They SALE believed OR DISTRIBUTIONthat bacteria arose spontaneously in a NOT FOR SALE OR DISTRIBUTION diseased patient; therefore, disease was inevitable and had nothing to do with bacteria or any microbes. This belief was called spontaneous generation. Pasteur had to discredit spontaneous generation to salvage his germ theory of disease. In an elegant series of experiments, Pasteur prepared nutrient-rich broth in a series of swan-neck© Jones flasks & Bartlett (so named Learning, because their LLC S-shaped necks resembled ©those Jones of swans). & Bartlett Learning, LLC PasteurNOT boiled FOR the SALE broth in OR the DISTRIBUTIONflasks, thereby destroying all microbes;NOT then heFOR left theSALE OR DISTRIBUTION flasks open to the air. However, the S-shaped neck trapped any microbes in the air and prevented their entry into the flasks. Thus, when the flasks were set aside to incubate in a warm environment, no microbes appeared in the broth (advocates of spontaneous © Jones &generation Bartlett assumed Learning, that microbes LLC would arise, because© airJones and the & so-calledBartlett life Learning, force LLC were being allowed in). Moreover, when the neck was cut off a flask and microbes from NOT FORthe SALE air dropped OR DISTRIBUTION into the broth, the broth soon becameNOT cloudy FOR with SALE microbial OR growth. DISTRIBUTION It was clear that the microbes were in the air and were not spontaneously arising from nutrients in the broth. Pasteur’s classic experiment is illustrated in FIGURE 1.7 . Pasteur’s work brought to an end a long and tenacious debate on spontaneous generation begun two© centuriesJones & earlier. Bartlett Moreover, Learning, his work LLC showed that microbes © Jones & Bartlett Learning, LLC could cause disease. ButNOT Pasteur FOR was SALE stymied OR by DISTRIBUTION his inability to obtain a pure culture NOT FOR SALE OR DISTRIBUTION by cultivating one type of bacterium apart from other types. In an effort to help French industry once again, he turned his attention to pébrine, a disease of silkworms. In 1865, he identified a protozoan infesting the silkworms and, by separating healthy silkworms© Jones from & diseased Bartlett ones Learning, and their food, LLC managed to quell the spread© Jones of the & dis- Bartlett Learning, LLC ease. Still the definitive proof eluded him. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Robert Koch Although Pasteur failed to relate a specific organism to a specific human disease, his work stimulated others to investigate the association of microbes with disease. Among © Jones &them Bartlett was Robert Learning, Koch, a LLC country doctor from East Prussia© Jones (now & partBartlett of Germany) Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

16 CHAPTER 1 The Microbial World: Surprising and Stunning

© Jones & Bartlett Learning, LLC Flask open© Jones & Bartlett Learning,Pasteur: LLC The broth provides to air a nutrient medium for the NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONgrowth of unseen organisms in the air: life comes from other life. Time passes His critics: A sterilized broth gives rise to life: © Jones & Bartlett Learning, LLC s©pont Jonesaneous gener & Bartlettation. Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (a) Sterile broth Organisms appear

Each experiment begins with Flask sealed sterilized broth. Any living things the broth may have Pasteur: The heat has killed ©contained Jones have & beenBartlett Learning, LLC © Jones & Bartlettthe microorg Learning,anisms in the LLC destroyed by heat. air. NOT FOR SALE OR DISTRIBUTION Time NOT FOR SALE OR DISTRIBUTION passes His critics: Sealing the flask prevents entry of the “life force.”

(b) Sterile broth No organisms appear © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Air entering is constantly Pasteur: The heat has killed sterilized the microorganisms in the air.

Time His critics: Sterilizing the air © Jones & Bartlett Learning,passes LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION killNOTs the “lifeFOR force.” SALE OR DISTRIBUTION

(d) Sterile broth No organisms appear

Pasteur: No living thing will appear in the flask because © Jones & Bartlett Learning, LLC microorganisms will© not Jones & Bartlett Learning, LLC FIGURE 1.7 Pasteur andNOT the SpontaneousFOR SALE Generation OR DISTRIBUTION be able to reach theNOT broth. FOR SALE OR DISTRIBUTION Controversy. Louis Pasteur engaged in a series of experiments His critics: If the “life force” to show that spontaneous generation is not a valid doctrine. has free access to the flask, Pasteur’s experiments and the objections of his critics are dis- life will appear, given enough played. (a) When a flask of sterilized broth is left open to the air, time. organisms© Jones appear. & (b Bartlett) When a flask Learning, of sterilized brothLLC is boiled © Jones & Bartlett Learning, LLC and sealed, no living things appear. (c) When air entering a flask Some days later the flask is of sterilizedNOT FOR broth is SALE heated withOR a DISTRIBUTIONflame, no living things appear. NOTstill free FOR of any SALE living thing. OR DISTRIBUTION (d) Broth sterilized in a swan-neck flask is left open to the air. Pasteur has disproved the The curvature of the neck traps dust particles and microbes, doctrine of spontaneous preventing them from reaching the broth. generation.

The Golden Age of Microbiology 17 A CLOSER LOOK © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEJams, ORJellies, DISTRIBUTION and Microorganisms NOT FOR SALE OR DISTRIBUTION 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 this by solidifying beef broth with gelatin. When inoculated onto the surface of the nutritious medium, bacterial cells grew vigorously© at Jonesroom temperature & Bartlett and produced Learning, discrete, LLC visible colonies. © Jones & Bartlett Learning, LLC On occasion, however, Koch was dismayed to find that the gelatin turned to liquid. It appeared that certainNOT bacterial FOR speciesSALE were OR producing DISTRIBUTION a chemical substance to NOT FOR SALE OR DISTRIBUTION digest the gelatin. Moreover, gelatin liquefied at the warm incubator temperatures commonly used to cultivate certain bacterial species. Walther Hesse, an associate of Koch’s, mentioned the problem to his wife and laboratory© Jones assistant, & Fannie Bartlett Eilshemius Learning, Hesse. SheLLC had a possible solution. For© years, Jones she & Bartlett Learning, LLC had been using a seaweed-derived powder called agar (pronounced ah′gar) to solidify herNOT jams andFOR jellies. SALE Agar ORwas valuableDISTRIBUTION because it mixed easily with most NOTliquids FORand, SALE OR DISTRIBUTION once gelled, 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 © Jones & Bartletthis paper on Learning, the isolation LLC of the bacterial organism responsible© Jones for tuberculosis.& Bartlett It Learning, is LLC noteworthy that Fannie Hesse may have been among the first Americans (she was NOT FOR SALEoriginally OR from DISTRIBUTION New Jersey) to make a significant contributionNOT FORto microbiology. SALE OR DISTRIBUTION 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 (see A Closer Look above).NOT FOR Koch’s SALE primary OR interest DISTRIBUTION was anthrax, a deadly blood dis- NOTanthrax FORAn SALE infection OR with DISTRIBUTION the ease in cattle and sheep (now known as a weapon of bioterrorists). bacterium Bacillus anthracis. Koch was determined to learn all he could about anthrax. In 1875, in a makeshift laboratory in his home, he injected mice with the blood of sheep that had died from anthrax.© Jones He then & performed Bartlett meticulousLearning, autopsies LLC and noted that the same© Jones symptoms & Bartlett Learning, LLC appearedNOT regularly FOR SALE in the mice.OR DISTRIBUTION Next, he magnified a blood specimen underNOT his FOR micro- SALE OR DISTRIBUTION scope and observed rod-shaped bacteria, all apparently of the same type. Determined to cultivate the bacteria, he visited the local butcher and obtained the eye of a cow, from which he obtained the clear fluid in the inner chamber. Then, while peering intently through his microscope, he successfully separated a few anthrax bacteria © Jones &from Bartlett the sheep Learning, blood and LLC added them to the clear fluid.© Jones Next, he & watched Bartlett for Learning, hours LLC NOT FORas SALE the bacteria OR DISTRIBUTION elongated, multiplied, formed tangledNOT threads, FOR and SALE reverted OR to highlyDISTRIBUTION resistant bodies called spores. At this point, Koch took some spores on a sliver of wood and injected them into healthy mice. Several hours later, the symptoms of anthrax appeared. Koch excitedly autopsied the mice and found their blood swarming with anthrax bacteria. The© cycle Jones was &complete. Bartlett Learning, LLC © Jones & Bartlett Learning, LLC A year later, KochNOT presented FOR his SALE work ORat the DISTRIBUTION University of Breslau. The scientists NOT FOR SALE OR DISTRIBUTION were astonished. Here was the verification of the germ theory of disease that had escaped Pasteur. Koch’s procedures came to be known as Koch’s postulates. These tech- niques, illustrated in FIGURE 1.8 , were adopted as a guide for relating specific microbes to specific diseases. They are still used today for this purpose. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION The Golden Age of Microbiology Golden Age of Microbiology A period of about 60 years during The science of microbiology blossomed during a period of about 60 years, now referred which the science of microbiology blossomed, beginning in to as the Golden Age of Microbiology. This period began in 1857 with Pasteur’s pro- 1857 with Pasteur’s proposal of © Jones &posal Bartlett of the germLearning, theory of LLC disease, and it continued into© Jones the twentieth & Bartlett century, Learning, until theLLC germ theory of disease. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

18 CHAPTER 1 The Microbial World: Surprising and Stunning

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Postulate 2 Anthrax bacillus Spore The microbes are isolated from the tissues of a dead animal, and a pure © Jones & Bartlett Learning,culture is prep LLCared. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOTPostulate FOR 4 SALE OR DISTRIBUTION The identical microbes are isolated and recultivated from the tissue specimens of the experimental © Jones & Bartlett Learning, LLC © Jones & Bartlettanima l.Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Postulate 3 Microbes from the pure culture are inoculated © Jones & Bartlettinto a he Learning,althy animal. The LLC © Jones & Bartlett Learning, LLC NOT FOR SALEdise asORe is DISTRIBUTIONreproduced. NOT FOR SALE OR DISTRIBUTION FIGURE 1.8 A Demonstration of Koch’s Postulates. Koch’s postulates are used to relate a single microbe to a single disease. The photo shows the rods of the anthrax bacillus as Koch observed them. Many rods are swollen with spores.

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE ORthe DISTRIBUTION advent of World War I. During theseNOT years, FOR numerous SALE branches OR DISTRIBUTION of microbiology were established, and the foundations were laid for the maturing process that has led to the modern science. During the Golden Age, a lively competition sprang up between France and © Jones & Bartlett Learning, LLCGermany to see which country© Jones would & leadBartlett the newly Learning, emerging LLC field of microbiology. For example, Koch presented his work in 1876, and within 2 years, Pasteur reported NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION that some types of bacteria were temperature-sensitive: Chickens did not acquire anthrax at their normal body temperature of 42°C, but did so when the animals were cooled down to 37°C. Then, in 1880, Pasteur found that he could enfeeble the bacteria associated with chicken cholera and inject them into healthy chickens, where © Jonesthey & protected Bartlett the Learning, animals against LLC a lethal dose of the bacteria.© Jones This & principle Bartlett is Learning,the LLC NOT FORbasis forSALE today’s OR vaccines. DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Pasteur’s experiments encouraged France to take the microbiological lead. However, Koch soon isolated the microbe that causes tuberculosis, and his coworkers were the first to cultivate the bacteria that cause typhoid fever and diphtheria. Before long, © Jones & Bartlett newsLearning, came from LLC France that scientists in Pasteur’s© Jones lab & had Bartlett linked diphtheria Learning, to aLLC chemical poison, a toxin, which is produced by the bacterium that the Germans had dis- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION covered. In later years, Koch’s coworker Emil von Behring successfully treated diphtheria in patients by injecting antitoxin, a preparation of blood proteins obtained from animals immunized against diphtheria. For his work, von Behring was awarded the first Nobel Prize in Physiology or Medicine. A Closer Look on page 19 describes the his- © Jones & Bartlett Learning, LLCtory of this prestigious award.© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Golden Age of Microbiology 19 A CLOSER LOOK © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALEThe Nobel OR DISTRIBUTIONPrize NOT FOR SALE OR DISTRIBUTION The Nobel Prizes are among the world’s most venerated awards. They were first conceived as a gesture of peace by a man whose discovery had unintentionally added to the destructive forces of warfare. Alfred Bernhard Nobel© Jones was the & third Bartlett son of aLearning, Swedish munitions LLC expert. As a young © Jones & Bartlett Learning, LLC engineer, he developed an interest in nitroglycerine, an oily substance 25 times more explosive than gunpowder.NOT FORIn 1863, SALE Nobel ORobtained DISTRIBUTION a patent for a detonator of mer- NOT FOR SALE OR DISTRIBUTION cury fulminate, and within 4 years, he used it to ignite solid nitroglycerine mixed with a type of sandy clay. The mixture was called dynamite, from the Greek dynamis meaning “power.” ©Dynamite Jones had & aBartlett clear advantage Learning, over other LLC explosives because it could© be Jones trans- & Bartlett Learning, LLC ported easily and handled with less fear. It became an overnight success and was adaptedNOT toFOR applications SALE in OR mining, DISTRIBUTION tunnel construction, and bridge and roadNOT building. FOR SALE OR DISTRIBUTION Before long, dynamite was being used in armaments on the battlefield. Nobel soon amassed a fortune through the control of several European companies that produced dynamite. However, toward the end of his life, he became a pacifist and © Jones & Bartlettbegan speaking Learning, out against LLC the use of his explosive in warfare.© Jones In 26 & lines Bartlett of his hand- Learning, LLC written will, Nobel directed that the bulk of his estate should be used to award prizes NOT FOR SALEthat would OR promote DISTRIBUTION peace, friendship, and service to humanity.NOT FOR SALE OR DISTRIBUTION After his death in 1896, the governments of Sweden and Norway established Nobel Prizes in five categories: chemistry, physics, physiology or medicine, literature, and peace. A sixth category, economics, was added in 1969. Every year, Nobel laureates assemble in Oslo or Stockholm© Jones on & December Bartlett 10, Learning, the anniversary LLC of Nobel’s death. Each © Jones & Bartlett Learning, LLC laureate receives a medallion,NOT FOR a scroll, SALE and ORall or DISTRIBUTION part of a cash award currently valued NOT FOR SALE OR DISTRIBUTION at about $1 million per category. The first Nobel Prize winners were announced in 1901. Among the recipients were Wilhelm K. Roentgen, the discoverer of x-rays; Jean Henri Dunant, the founder of the Red Cross; and Emil von Behring, the developer of the diphtheria antitoxin. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

By the turn of the century, microbiology had become international in scope, mov- ing far beyond France and Germany: Ronald Ross, an English physician working in © Jones &the Bartlett Far East, provedLearning, that mosquitoes LLC transmit the microbes© Jones that cause & Bartlett malaria; anotherLearning, LLC Englishman, David Bruce, showed that tsetse flies transmit sleeping sickness and NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION opened the African continent to colonization; and the Japanese investigator Masaki Ogata reported that rat fleas transmit bubonic plague, thereby solving the centuries- old mystery of how plague spread. American microbiologists were represented by Howard Taylor Ricketts, who located the agent of Rocky Mountain spotted fever in the human bloodstream© Jones and demonstrated & Bartlett its Learning, transmission LLC via ticks; and by Walter © Jones & Bartlett Learning, LLC Reed, who led a contingentNOT FORto Cuba SALE to pinpoint OR DISTRIBUTION mosquitoes as the insects that trans- NOT FOR SALE OR DISTRIBUTION mit yellow fever. His discovery led to the mosquito eradication programs that made possible the building of the Panama Canal. Reed and his group are portrayed in FIGURE 1.9 . Amid© Jones the burgeoning & Bartlett interest Learning, in microbes, LLC other scientists devoted© Jones research & toBartlett Learning, LLC their environmental importance. The Russian scientist Sergius Winogradsky, for exam- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION ple, discovered that certain bacteria use carbon dioxide to synthesize sugars, much as plants do in the process of photosynthesis. And Martinus Beijerinck, a Dutch investigator, isolated bacteria that trap nitrogen in the soil and make it available to plants for use in constructing amino acids and proteins. It was clear that interest in microbes © Jones &was Bartlett reaching Learning, far beyond theirLLC importance in medicine.© Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

20 CHAPTER 1 The Microbial World: Surprising and Stunning

FIGURE 1.9 Finding the Cause of Yellow Fever. A painting by Robert Thom depicting members of the 1900 yellow fever commission in Cuba at the bedside of Private John Kissinger. Kissinger allowed himself to be bitten by mosquitoes after they had bitten yellow fever patients. When asked why he and © Jones & Bartlett Learning, LLCothers were participating in the© hazardous Jones experiments, & Bartlett Kissinger Learning, replied: “We LLC volunteer solely for the NOT FOR SALE OR DISTRIBUTIONcause of humanity and in the interestNOT ofFOR science.” SALE Left toOR right: DISTRIBUTION Major W. C. Gorgas, Aristides Agaramonte, Carlos J. Finlay, James Carroll, and Walter Reed.

© Jones &Into Bartlett the Twentieth Learning, CenturyLLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION With the advent of World War I, scientists turned to research on blood products and vaccines to treat and prevent war-related infections. In the postwar years, scientists researched the key roles that microbes play in industrial processes. For example, food microbiologists identified the processes by which microbes manufacture numerous © Jones & Bartlett dairyLearning, products. LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONWork with viruses expanded greatly duringNOT FOR the 1930s SALE and OR 1940s DISTRIBUTION with the inven- tion of the electron microscope. An ordinary light microscope permits magnifications of 1,000 times, while the electron microscope permits magnifications of 100,000 times. The mysterious viruses could now be visualized for the first time, and an intense © Jones & Bartlett Learning, LLCperiod of research in virology© Jones ensued & (ChapterBartlett 5).Learning, Also about LLC that time, antibiotics were discovered, and physicians were presented with previously unimagined thera- NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION pies for established cases of disease. In the period after World War II, large sums of money became available for biochemical research, and scientists worked out the key processes by which microbes synthesize proteins. These processes are centered in the hereditary units called genes, © Jonesand &soon Bartlett the discipline Learning, of microbial LLC genetics was in full flower.© Jones Elegant & Bartlett applications Learning, LLC NOT FORof this SALE research OR were DISTRIBUTION realized in the 1970s, with the adventNOT of genetic FOR engineering SALE OR and DISTRIBUTION biotechnology. Scientists learned to isolate genes, manipulate and splice them, and control the biosynthetic processes that genes oversee in microbial cells. With the seminal discoveries in gene research, the Age of Molecular Genetics © Jones & Bartlett dawned,Learning, and LLCtoday we are experiencing the© fruitsJones of that& Bartlett age. We liveLearning, in a world LLC where bacteria are engineered to destroy pollutants, where yeasts are reconfigured to produce NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION human proteins, and where viruses carry therapeutic genes into patients with inher- ited diseases. Nor does the harvest end here. Scientists continue to dream of genetically modified plants that are rich enough in protein to resolve the world’s shortage of this nutrient; they have given us new tests that dramatically reduce the time to diag- © Jones & Bartlett Learning, LLCnose disease; and they are© just Jones beginning & Bartlett to ponder Learning, the implications LLC of knowing the NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Microbial World 21 intricate details of the human genome (Chapter 4). Truly, they have changed the face © Jones & Bartlett Learning, LLC © Jones of& science.Bartlett Learning, LLC NOT FOR SALEAnd theOR microbe DISTRIBUTION stands at the center of all theseNOT discoveries FOR SALE and ORadvances. DISTRIBUTION Microbiology is a very hot topic in today’s world, and you are fortunate to be studying this discipline of biology. Microbiologists range from the research scientist to the food technologist to the environmental scientist; they include the individuals who study industrial microbiology,© Jones agriculture,& Bartlett andLearning, medicine. LLC Microbiology penetrates © Jones & Bartlett Learning, LLC virtually every aspect NOTof our existence,FOR SALE and asOR we DISTRIBUTION shall see time and time again, microbes NOT FOR SALE OR DISTRIBUTION are essential elements for improving the quality of our society and our lives.

The© Jones Microbial & Bartlett World Learning, LLC © Jones & Bartlett Learning, LLC The microbialNOT FOR world SALE includes OR DISTRIBUTIONa diverse variety of organisms that inhabitNOT most FOR envi- SALE OR DISTRIBUTION ronments on Earth. This world is the subject matter of the discipline of microbiology and this book. The microbes are extremely diverse, as the following paragraphs will illustrate. © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORBacteria SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Among the best known of all microbes are the bacteria. Not only are the bacteria important in research and clinical medicine, but they are also vital to many benefi- cial activities that take place in the environment. They recycle the elements in dead and decaying matter, purify many of our waterways, and produce numerous foods we eat. A collection of bacteria© Jones magnified & Bartlett thousands Learning, of times LLC with an electron micro- © Jones & Bartlett Learning, LLC scope is shown in FIGURENOT 1.10 FOR . SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Bacteria have existed on Earth for approximately 3.5 billion years. Over this extraordinarily long period of time, they have evolved to occupy every conceivable niche on Earth. For instance, various species live in the outer reaches of the atmosphere,© Jonesat the bottoms & Bartlett of the Learning, oceans, in the LLC frigid valleys of the Antarctic© Jones continent, & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

FIGURE 1.10 Mixed Bacteria. A false color image of mixed bacteria. Rod and spherical forms in various sizes are visible in this view. The bacteria shown here have been color enhanced to help distinguish © Jones &them. Bartlett These bacteria Learning, are not this LLC color normally. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

22 CHAPTER 1 The Microbial World: Surprising and Stunning and in the scalding hot deserts of Africa. No other organism of any kind (including © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLChumans) have adapted so thoroughly to Earth’s varied conditions. NOT FOR SALE OR DISTRIBUTIONAs we discuss in ChapterNOT 5, FOR most SALE bacteria OR fit intoDISTRIBUTION three broad groups according to their shapes. There are rod-shaped bacteria, spherical bacteria, and spiral bacteria. Many bacterial species are heterotrophic—that is, they acquire their food from organic matter. Some species are autotrophic—they can synthesize their own food from basic © Joneselements. & Bartlett Most speciesLearning, of bacteria LLC utilize oxygen in their© chemistry, Jones & but Bartlett the bacteria Learning, LLC NOT FORexisting SALE in oxygen-poor OR DISTRIBUTION environments are also important.NOT In tightly FOR compacted SALE OR land- DISTRIBUTION fills, for instance, such bacteria decay the garbage and recycle the elements for reuse by other organisms. As we mentioned earlier, many species of bacteria contribute to society in the food © Jones & Bartlett industry,Learning, in the LLC industrial plant, on the farm,© andJones in the & genetic Bartlett engineering Learning, lab. In LLC addi- NOT FOR SALE ORtion, DISTRIBUTION bacteria make their presence felt in theNOT environment. FOR SALE Certain OR DISTRIBUTIONspecies, for example, live on the roots of pod-bearing plants called legumes. Here, they extract nitrogen from the air and make it available to the plants. The plants then use the nitrogen to construct the proteins they need, which are also needed by animals, including humans. Unfortunately, many species of bacteria are involved in disease. Using their con- © Jones & Bartlett Learning, LLCsiderable powers of reproduction© Jones and & theirBartlett ability Learning, to overcome LLC body defenses, bacte- NOT FOR SALE OR DISTRIBUTIONria can infect vital tissuesNOT or organ FOR systems SALE and OR bring DISTRIBUTION on illness and death. Moreover, certain bacterial species produce toxins that interfere with physiological processes in the body. For example, the toxin produced by the botulism microbe interrupts the pas- sage of impulses between nerve and muscle cells. Inhibition of muscle contraction fol- © Joneslows, & and Bartlett in many Learning, situations, paralysisLLC and death ensue. We© Jonesstudy bacterial & Bartlett disease Learning, in LLC NOT FORChapter SALE 18. OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Protozoa Protozoa are a diverse group of microbes that differ substantially from the bacteria and viruses in their structural composition. For example, protozoal cells have nuclei, © Jones & Bartlett whileLearning, bacterial LLC cells do not. In addition, protozoal© Jones cells & haveBartlett in their Learning, cytoplasm aLLC series NOT FOR SALE ORof DISTRIBUTION ultramicroscopic cellular bodies. PartlyNOT for theseFOR reasons,SALE ORprotozoa DISTRIBUTION are classified separately from the bacteria and viruses. The diversity of protozoa is illustrated in FIGURE 1.11 . Protozoa have been used for decades as research tools. For example, the flagellar © Jones & Bartlett Learning, LLCmotion exhibited by these© microbes Jones &is quiteBartlett similar Learning, to that of human LLC sperm cells, and the information gleaned from protozoal studies can be used to help scientists better NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION understand how sperm cells move. Many species of protozoa live freely in the environment and break down the remains of plants and animals and recycle their com- ponents. And certain protozoa are photosynthetic—they trap the sun’s energy and transform it into the chemical energy of carbohydrates (sugars). These protozoa serve © Jonesas food & Bartlett sources for Learning, other organisms LLC in Earth’s waters. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Algae alga (pl. algae) An organism The term algae is not a formal biological term; rather, it implies a large group of in the kingdom Protista that photosynthetic organisms, some of which are microscopic and relatively simple. performs photosynthesis. © Jones & Bartlett TheLearning, simple algae LLC are plantlike in that they© Jones contain & photosynthetic Bartlett Learning, pigment LLC molecules, but they are considered microbes because they are single-celled (unicellular) NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION organisms. Several freshwater species of unicellular algae exist, but most species are found in marine environments. Two important algal groups, the diatoms and dinoflagellates, inhabit the oceans in astronomical numbers, where they form the bases of many © Jones & Bartlett Learning, LLCfood chains. The diatoms© and Jones dinoflagellates & Bartlett utilize Learning, their photosynthetic LLC pigments NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

The Microbial World 23

Sucker device © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Flagella NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (c) FIGURE 1.11 Three Species of Protozoa. Electron micrographs of three species of protozoa illustrating differences in shape and size. (a) The amoeba Naegleria fowleri, a cause of meningitis in humans. Note the irregular shape of this organism. (b) A protozoan called a trypanosome. The elongated shape and hairlike appendage (flagellum) are apparent. This organism causes African sleeping © Jones &sickness. Bartlett (c) Another Learning, flagellated LLC protozoan, Giardia lamblia (×8062).© Jones The organism & Bartlett has a flat shape Learning, with multiple LLC flagella extending NOT FORtoward SALE the rear.OR TheDISTRIBUTION protozoan on the left shows the sucker deviceNOT on its FOR lower surface SALE for ORholding DISTRIBUTION fast to tissue. Giardia causes diarrhea in humans.

to trap sunlight’s energy and convert it to carbohydrates’ energy for consumption by other organisms. Scientists© Jones estimate & Bartlett that the microscopic Learning, algae LLC of the oceans trap more © Jones & Bartlett Learning, LLC energy, use more carbonNOT dioxide, FOR SALEand produce OR DISTRIBUTION more oxygen than all the land plants NOT FOR SALE OR DISTRIBUTION and other algae combined. Simple algae have also been investigated as possible food sources for expanding world populations. The algae are cultivated in massive tanks; they are then dried and added© toJones such things & Bartlett as ice cream Learning, and yogurt LLC to enhance the nutrient© content. Jones Algae & Bartlett Learning, LLC used as food are often referred to as single-cell protein (or SCP). Chapter 7 explores NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION these microbes in depth. Algae do not infect humans; however, algae can be the cause of serious poisoning. Shellfish and fish bioaccumulate algal products that can be toxic to humans. When people eat the contaminated seafood, the algal toxins can cause serious neurological © Jones &dysfunction. Bartlett Learning,Freezing and LLC cooking will not neutralize© these Jones toxins, & Bartlett so contaminated Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

24 CHAPTER 1 The Microbial World: Surprising and Stunning food must be avoided. In addition to harming humans, algal blooms can cause mas- © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLCsive fish kills. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Fungi Fungi are among the major decomposers of organic matter on Earth. They are dis- tinguished from other microbes by their physical structure and by the way they © Jonesobtain & Bartlett nutrients: Learning, They secrete LLC enzymes into the environment© Jones and &break Bartlett down Learning,the LLC NOT FORnearby SALE organic OR matter. DISTRIBUTION Then, they absorb the molecular NOTparticles FOR of matter SALE through OR DISTRIBUTION their cell membranes. Other microbes take up small molecules directly from the environment. Although their cells are microscopic, fungi are considered by many biologists to © Jones & Bartlett beLearning, multicellular LLC organisms. This is because© Jones the body & ofBartlett a fungus Learning, consists primarily LLC of cells joined in long, tangled filaments, as pictured under the electron microscope NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION in FIGURE 1.12 . These filaments, called hyphae, form networks that are visible to the unaided eye; the network is called a mycelium (the term “mold” is commonly used for the mycelium of a fungus). Other species of fungi consist of single cells lacking a filamentous arrangement. These single-celled fungi, known as yeasts, are central to © Jones & Bartlett Learning, LLCthe bread and spirits industries,© Jones as we & describeBartlett in Learning, Chapters 8 LLCand 12. NOT FOR SALE OR DISTRIBUTIONInstances abound whereNOT fungi FOR benefit SALE society. OR DISTRIBUTION For example, one mold called Aspergillus Aspergillus is used to produce the alcoholic rice beverage called sake, and another a-spe˙ r-jil′lus mold named Claviceps is cultivated to produce drugs that help relieve migraine Claviceps headaches. Unfortunately, many species of fungi are agricultural pests, causing grave kla′vi-seps © Joneseconomic & Bartlett damage Learning, to farmers. Indeed,LLC a funguslike microbe© called Jones a water & Bartlett mold caused Learning, LLC the Great Irish Potato Famine of 1845–1852, a disaster that changed the face of two NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION continents. Chapter 8 chronicles that story. Fungi also can cause serious disease in humans, other animals, and plants. In humans and animals, fungi can infect the skin, mucous membranes, urinary tract, bone, liver, spleen, etc., and can obviously be the cause of serious disease. Fungi © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION (a) (b) FIGURE 1.12 The Fungus Aspergillus niger. (a) A scanning electron micrograph showing the moldlike phase of Aspergillus niger. Many stalk-like conidiophores are present within the mycelium. Conidiophores contain conidia, the unprotected spores of the fungus. This photograph demonstrates the three-dimensional image possible with the scanning electron microscope. (b) A close-up view of © Jones & Bartlettone conidiophore Learning, with a mass LLC of conidia. © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Questions to Consider 25 can infect plants, including crops. Because the same group of fungi can infect both © Jones & Bartlett Learning, LLC © Jones humans& Bartlett and Learning,plants, crop LLCinfection with fungi is a potential source of infection for NOT FORpeople. SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Viruses Although most people are familiar with the word “virus,” few people are aware of the characteristics of a virus.© Jones Viruses & consistBartlett of aLearning, fragment of LLC nucleic acid encased in a © Jones & Bartlett Learning, LLC coating of protein. InNOT some FORcases, SALEa membranous OR DISTRIBUTION envelope encloses the protein coat. NOT FOR SALE OR DISTRIBUTION Viruses do not grow; they produce no waste products; they display none of the chemical reactions we associate with living things; and they are unable to reproduce inde- pendently of a host cell. But viruses do reproduce actively within their host cells, and in doing so, they use the© Joneschemical & machineryBartlett Learning, of the cells LLCfor their own purposes. Some© Jones minutes & toBartlett Learning, LLC hoursNOT later, FOR hundreds SALE of newOR virusesDISTRIBUTION exit from each cell, often leavingNOT in their FOR wake SALE OR DISTRIBUTION disintegrated host cells. As this wave of cell destruction spreads, the tissue suffers damage and the symptoms of disease ensue. We define and discuss the characteristics of viruses in more depth in Chapter 6. © Jones & BartlettDespite theirLearning, role in causingLLC infectious disease (e.g.,© Jones hepatitis, & Bartlettinfluenza, Learning, AIDS), LLC NOT FORviruses SALE perform OR DISTRIBUTION some valuable services to medical science.NOT For FOR example, SALE the OR virus DISTRIBUTION that normally causes common colds has been genetically altered to make it less infectious, then programmed to carry the genes that relieve the symptoms of cystic fibrosis. Patients with cystic fibrosis have damaged genes that encourage mucus buildup in their airways and, consequently, difficulty in breathing. The genetically altered cold virus ferries cor- rect copies of the genes© intoJones the respiratory& Bartlett tract Learning, cells, and theLLC proteins encoded by the © Jones & Bartlett Learning, LLC genes relieve the mucusNOT accumulation. FOR SALE Soon, OR normal DISTRIBUTION breathing is restored. We shall see NOT FOR SALE OR DISTRIBUTION many more instances of how microbes benefit us as we move through the chapters ahead.

©A JonesFinal Thought & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION It should be clear from this chapter that microbes, despite their involvement in disease, contribute substantially to the quality of life in our society. Rather than gush with enthusiasm on the positive roles they play, I prefer to paraphrase several concepts of applied microbiology set down by the late industrial microbiologist David Perlman of the © Jones & UniversityBartlett of Learning, Wisconsin. In LLC a 1980 publication, Perlman wrote:© Jones & Bartlett Learning, LLC NOT FOR SALE1. TheOR microbe DISTRIBUTION is always right, your friend, and a sensitiveNOT FOR partner; SALE OR DISTRIBUTION 2. There are no stupid microbes; 3. Microbes can and will do anything; 4. Microbes are smarter, wiser, and more energetic than chemists, engineers, and others; and © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 5. If you take care of your microbial friends, they will take care of your future. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

Questions to Consider © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT1. In FOR her biography SALE of OR Louis DISTRIBUTION Pasteur, Patrice Debré describes Pasteur’sNOT 1857 paperFOR on SALE OR DISTRIBUTION lactose fermentation of milk as “the birth certificate of microbiology.” Why do you suppose she thinks so highly of the paper? Further, she writes that as a result of the “Pasteurian revolution,” medicine could no longer do without science, and hospitals could no longer be mere hospices. What does she have in mind? © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION

26 CHAPTER 1 The Microbial World: Surprising and Stunning

© Jones & Bartlett Learning, LLC 2. “Microbes? All they© doJones is make & you Bartlett sick!” From Learning, your introduction LLC to microbes in NOT FOR SALE OR DISTRIBUTION this chapter, howNOT might FORyou counter SALE this OR argument? DISTRIBUTION 3. Every now and then in science, a seminal experiment sets off a barrage of studies that lead to the discovery of an important principle. Which experiment do you believe was the spark that ultimately led to our understanding of the germ theory of disease? © Jones &4. BartlettIf you were Learning, to ask someone LLC to describe a microbe, he© or Jones she might & thinkBartlett of a Learning, LLC NOT FOR SALEdot underOR DISTRIBUTIONa microscope. However, the microbial worldNOT is quite FOR varied, SALE and eachOR DISTRIBUTION of its members is unique. Although your experience in microbiology is somewhat limited at this juncture, the information in this chapter should give you some insight into the microbial world. How, then, would you now describe a microbe? 5. This chapter noted two reasons why interest in microbes ebbed after the death © Jones & Bartlett Learning,of van LLC Leeuwenhoek. Can you think© of Jones any other & reasons? Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION6. The poet John Donne once wrote: “NoNOT man FOR is an island,SALE entire OR ofDISTRIBUTION itself.” This maxim applies not only to humans, but to all living things in the natural world. What are some roles microbes play in the interrelationships among living things? 7. Our world is somewhat “germ-phobic.” The media cover new outbreaks of disease, we eagerly await new antibacterial medicines, and we hear of new ways © Jones & Bartlett Learning, LLC to “fight germs.” ©But Jones suppose & there Bartlett were no Learning, microbes to contendLLC with. What do NOT FOR SALE OR DISTRIBUTION you suppose life wouldNOT be FOR like? SALE OR DISTRIBUTION

© Jones &Key Bartlett Terms Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Informative facts are necessary for the expression of every concept, and the information for a concept is founded in a set of key terms. The following terms form the basis for the concepts of this chapter. On completing the chapter, you should be able to explain or define each one: © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTIONalgae NOTgene FOR probe SALE OR DISTRIBUTION anthrax germ theory of disease antibody Golden Age of Microbiology Anton van Leeuwenhoek Louis Pasteur bacteria microbe © Jones & Bartlett Learning, LLCbioremediation © Jones & Bartlettprotozoa Learning, LLC NOT FOR SALE OR DISTRIBUTIONbiotechnology NOT FOR SALERobert OR KochDISTRIBUTION fermentation virus fungi

To explore these topics in more detail, visit this book’s Student Companion Web Site at http://microbiology.jbpub.com/microbes/3e. The site features chapter outlines, study © Jones & Bartlett Learning,quizzes, an interactiveLLC glossary, animated flashcards,© Jones crossword & Bartlett puzzles, Learning, and links toLLC news, research, and reference sites on the Web. NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION