Microbiology: Then and Now PDF

CHAPTER 1 CHAPTER PREVIEW Microbiology: 1.1 The Discovery of Microbes Leads t...

CHAPTER 1 CHAPTER PREVIEW Microbiology: 1.1 The Discovery of Microbes Leads to Questioning Their Origins Microbiology Pathways: Being Then and Now a Scientist Investigating the Microbial World 1: Can Life Arise Spontaneously? MicroInquiry 1: Scientific Inquiry and Spontaneous Generation Space. The final frontier Really The final frontier The image on the right in the chapter opening illus- 1.2 Disease Transmission Can Be Prevented tration shows one of an estimated 350 billion large Clinical Case 1: Childbed Fever : A galaxies and more than 1024 stars in the visible uni- Historical Reflection verse. However, the invisible microbial universe on 1.3 The Classical Golden Age of Earth consists of more than 1030 microorganisms (or Microbiology Reveals the Germ microbes for short) distributed among an estimated 1 trillion (1012) species. As the image on the left 1.4 With the Discovery of Other Microbes, shows, microbes might be microscopic in size, but the Microbial World Expands they are magnificent in their evolutionary diversity 1.5 A Second Golden Age of Microbiology and astounding in their sheer numbers. Together, Involves the Birth of Molecular Biology we can refer to the global community of microbes and Chemotherapy and their genes as Earth’s microbiome. 1.6 A Third Golden Age of Microbiology Is Now A Day in the Life of a Microorganism Because microorganisms exist in such diversity and vast numbers in the oceans, landmasses, and atmo- The Oceans sphere, they must play important roles in the very The oceans and seas cover more than 70% of planet survival of other organisms on the planet. Conse- Earth and represent the foundation that maintains quently, could understanding these microscopic our planet in a habitable condition. A critical fac- organisms on Earth be as important as studying tor in this maintenance is the marine microbiome, stars and gala ies in space Let s uncover but a few which, composed of some 3 × 1029 microbes, dom- examples of what a “day in the life of a microorgan- inates ocean life. High densities of these organ- ism” is like in shaping the fundamental life pro- isms can be found anywhere from the frozen polar cesses around the globe. regions to the hot, volcanic thermal vents and the Photographic image of nearby galaxies in space (right) and a light microscope image (left) of bacterial cells (larger dots), viruses (smaller dots), and a diatom (center). (left) Courtesy of Jed Alan Fuhrman, University of Southern California. (right) Courtesy of JPL-Caltech/NASA. 2  Microbiology: Then and Now 3 cold seeps on the dark sea oor. Making up 90 of soil can have up to 1013 microbes living in the water- the ocean biomass, this marine microbiome is criti- filled pore spaces in the soil FIGURE 1.1B). cal to regulating life on Earth. This diverse soil microbiome is responsible for Every day, many of the dwellers in this microbial many daily activities essential to life. Here are some community perform the following: of the activities soil microorganisms perform: ▶ Create the foundation for all marine food ▶ Carry out 90% of all biochemical reactions webs by performing photosynthesis (in occurring in the soil. sunlit areas) and chemosynthesis (in dark ▶ Recycle dead plant and animal material and areas) to convert carbon into sugars and return carbon dioxide to the atmosphere. nutrients on which all fish and ocean mam- ▶ Represent a source for many of today s anti- mals directly or indirectly depend. biotics. ▶ Provide up to 50% of the oxygen gas we ▶ Provide plants with important nutrients, breathe and many other organisms use to such as nitrogen, sulfur, and phosphorus. stay alive by performing photosynthesis Think of it this way—microbes are helping (FIGURE 1.1A). to feed the world. ▶ Control atmospheric aerosols and cloud for- Microbes also can degrade pesticides and other mation through the sea spray ejected into synthetic pollutants contaminating the soil. Many the atmosphere. of these microbes have been “domesticated” for this ▶ Consume 50% of the dead plant and animal very role through a process called bioremediation. matter generated on Earth each year. As new species are identified and studied, the roles ▶ Operate as the engines that drive and control of the soil microbiome will be unraveled. nutrient and mineral cycling and that reg- ulate energy ow, both of which can affect The Atmosphere long-term climate change. Viruses are the most abundant infectious More than 315 different types of bacteria have been agents on Earth. There are an estimated 1031 viruses identified in air masses 10 kilometers above the in the oceans and most of these viruses remain Earth’s surface. These microbes along with fungal uncharacterized. However, they probably infect spores account for 20% of all particles—biological and marine microbes. Because many of these microbes non-biological—in the atmosphere (FIGURE 1.1C). are important in the activities listed above, viruses Although less studied than the ocean and soil micro- undoubtedly play an in uential role in the global biomes, scientists believe the atmospheric communi- cycling of nutrients and elements, such as carbon ties perform the following roles: and nutrients. In fact, infections by marine viruses ▶ Play an integral role with marine microbes are responsible for releasing and recycling some in the formation of water vapor (clouds). 150 gigatons of carbon per year. ▶ elp form raindrops and snow akes. Today, microbiologists around the world are ▶ Affect the chemical composition of the discovering many marine microbes that are new atmosphere. to science. What are the daily occupations of these ▶ In uence weather cycles, alter the com- and other mysterious microbes and viruses yet to position of rain and snow, and affect daily be identified and cataloged ndoubtedly, many weather patterns. play useful and probably intimate roles, the conse- Although we have much to learn and under- quences of which we have yet to discover. The scien- stand about microbes in the clouds, it is evident that tific studies are ust beginning. they help stabilize the atmosphere. The Land The Earth’s Subsurface Microbes on dry land are no less impressive in their Consider that the oceans, soil, and air represent only daily activities than their marine counterparts. In those environments most familiar to us. In fact, a fact, every time you walk on the ground, you step on diverse microbial workforce is being cataloged billions of microbes. Moreover, like their cousins in anywhere there is an energy source and water. For the oceans, they can be found in every imaginable example, scientists have drilled 2,400 meters into place, from the tops of the highest mountains to the the Earth’s subsurface on land or below the sea- deepest caves. In fact, a kilogram of moist garden oor. In the solid rock, they have discovered another 4 CHAPTER 1 MICROBIOLOGY: THEN AND NOW (A) (B) (C) (D) (E) FIGURE 1.1 Daily Life in the Microbial World. Microbes play many roles. For example, (A) photosynthetic microbes inhabit the upper sunlit layer of almost all oceans and bodies of fresh water where they produce food molecules that sustain the aquatic food web and generate oxygen gas. (Bar = 20 μm.) (B) In the soil, microbes degrade dead plants and animals, form beneficial partnerships with plants, and recycle carbon, nitrogen, and sulfur. (Bar = 5 μm.) (C) Besides their involvement in the formation of raindrops and snowflakes, microbes in the atmosphere are important for water vapor to condense into clouds that help cool the Earth. (D) Large numbers of microbes can be found on and in the body where most play beneficial roles for our health. (Bar = 2 μm.) (E) A few microbes have played disease roles and affected world health. This 1974 photo of a Bengali boy shows the effects of smallpox, which was responsible for 300–500 million deaths during the 20th century. »» What would happen to life on Earth if each of the examples above (A–D) was devoid of microbes? (A) © NNehring/E+/Getty Images. (B) © Science Photo Library/Shutterstock. (C) © Loskutnikov/Shutterstock. (D) © Science Photo Library/Getty Images. (E) Courtesy of Jean Roy/CDC.  Microbiology: Then and Now 5 frontier composed of microbes that are sealed off carrying out an amazing array of metabolic reac- from the rest of the world. These intraterrestrials tions to help us resist disease, regulate our diges- (microbes living in sediment and rock) are another tion, maintain a strong immune system—and even diverse workforce that, even buried in rock, are in uence our risk of obesity, asthma, and allergies. believed to make up more microbial biomass than To be human and healthy, we must share our daily that of all the microbes in water and soil. Scientists lives with this homegrown microbiome. believe these intraterrestrials also are involved with One aspect of a microbe’s daily life that we have the daily recycling of minerals and stabilizing the overlooked until now is its role in infectious disease. biogeochemical health of our planet. This omission was done on purpose because only a very small minority of microbes are responsible for Today, the workforce composing the global infections and disease. Although such disease-causing microbiome is still being cataloged and their num- agents, called pathogens, are rare, some, such as bers and daily activities keep growing. As Louis Pas- those causing diseases like plague, malaria, and teur, one of the fathers of microbiology, once stated, smallpox (FIGURE 1.1E), throughout history have “Life [plant and animal] would not long remain possi- swept through cities and villages, devastated popula- ble in the absence of microbes.” tions, killed great leaders and commoners alike, and, That need for microbes is evident even much as a result, have transformed politics, economies, and closer to home. Microbial communities inhabit the public health on a global scale. Nevertheless, as you bodies of all plants and animals. For animals, most read through the chapters of this text, remember only every species, from termites to bees, from cows to a small minority of microbes are dedicated pathogens. humans, has an intimate microbiome associated A major focus of this introductory chapter is to with it. For example, the human microbiome con- give you an introspective “first look” at microbiology— sists of some 40 trillion (40 × 1012) microbes, which then and now. We will see how microbes were first is about equal to the number of cells (30 × 1012) discovered and why infectious disease preoccupied building the human body. These outwardly invisible the minds and efforts of so many. Along the way, we strangers have established themselves since birth will see how curiosity and scientific inquiry stimu- as separate and unique communities of microbes on lated the quest to understand the microbial world the skin, in the respiratory tract, and especially in just as the science of microbiology does today, as the gut (FIGURE 1.1D). In fact, the human gut micro- described in the box MICROBIOLOGY PATHWAYS. To biome is essential for a healthy life. Although some begin our story, we reach back to the 1600s, where we are transient, most of the species spend each day encounter some very inquisitive individuals. Chapter Challenge Now that you have learned a little about the diverse global workforce of microorganisms, can you explain how the microbes were revealed and identify several challenges that some microorganisms pose for microbiology today? Let’s investigate! MICROBIOLOGY PATHWAYS Being a Scientist Science might not seem like the most glamorous profession. In fact, 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 the luck of the draw, but actually many scientists share a set of characteristics that puts them on the trail to success. Robert S. Root-Bernstein, a physiology professor at Michigan State University, points out that many prominent scientists like to goof around, play games, and surround themselves © Comstock/Thinkstock. (continues) 6 CHAPTER 1 MICROBIOLOGY: THEN AND NOW MICROBIOLOGY PATHWAYS (Continued) with a type of chaos aimed at revealing the unexpected. Their labs might appear to be in disorder, but they know exactly where every tube or bottle belongs. Scientists also identify intimately with the organisms or creatures they study (it is said that Louis Pasteur actually dreamed about microorganisms), and this 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 therefore had an appreciation of patterns.) The geneticist and Nobel laureate Barbara McClintock once remarked, “I was just so interested in what I was doing I could hardly wait to get up in the morning and get at it. One of my friends, a geneticist, said I was a child, because only children can’t wait to get up in the morning to get at what they want to do.” Clearly, another characteristic of a scientist is having a child-like curiosity for the unknown. Another Nobel laureate and immunologist, Peter Medawar, once said, “Scientists are people of very dissimilar temperaments doing different things in very different ways. Among scientists are collectors, classifiers, and compulsive tidiers-up; many are detectives by temperament and many are explorers; some are artists and others artisans. There are poet-scientists and philosopher-scientists and even a few mystics.” In other words, scientists come from all lifestyles. For this author, I too have found science to be an extraordinary opportunity to discover and understand something never before known. Science is fun, yet challenging—and at times arduous, tedious, and frustrating. As with most of us, we will not make the headlines for a breakthrough discovery or find a cure for a disease. However, as scientists we all hope our hard work and achievements will contribute to a better understanding of a biological (or microbiological) phenomenon and will push back the frontiers of knowledge and have a positive impact on society. Like any profession, being a scientist is not for everyone. Besides having a bachelor’s degree in biology or microbiology, you should be well read in the sciences and capable of working as part of an interdisciplinary team. Of course, you should have good quantitative and communication skills, have an inquisitive mind, and be goal oriented. If all this sounds interesting, 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 text, but you should also visit with your instructor. Simply stop by the student union, buy two cups of coffee, and you are on your way. KEY CONCEPT 1.1 The Discovery of Microbes Leads to Questioning Their Origins As the 17th century arrived, an observational revo- for the structure of cork. Seeing “a great many lit- lution was about to begin. A Dutch spectacle maker tle boxes,” he called these boxes cella (= rooms), and named Zacharias Janssen and others discovered that if from that observation today we have the word “cell” they combined two curved lenses together, they could to describe the basic unit of life. magnify small ob ects. Many individuals in olland, Micrographia represents one of the most impor- England, and Italy further developed this combination tant books in science history. It awakened the of lenses that in 1625 would go by the term microsco- learned and general population of Europe to the pio or “microscope.” This new invention would be the world of the very small, revolutionized the art of forerunner of the modern-day instrument. scientific investigation, and showed that the micro- scope was an important tool for unlocking the Microscopy—Discovery of the Very Small secrets of an unseen world: the world of the cell. Robert ooke, an nglish natural philosopher the At this same time, across the North Sea in Delft, term “scientist” was not coined until 1833), was one olland, Antoni van Leeuwenhoek, a successful of the most inventive and ingenious minds in the tradesman and dry goods dealer, was using hand history of science. As the curator of experiments lenses to inspect the quality of his cloth. As such, for the Royal Society of London, ooke published a and without any scientific training, Leeuwenhoek book in 1665, called Micrographia, in which he took became skilled at grinding single pieces of glass into advantage of the magnification abilities of the early fine magnifying lenses. Placing such a lens between microscopes to make detailed drawings of many two metal plates riveted together, Leeuwenhoek s living ob ects, including eas, lice, and peacock “simple microscope” could greatly out magnify feathers. Perhaps his most famous description was Hooke’s microscope (FIGURE 1.2A, B).  KEY CONCEPT 1.1 The Discovery of Microbes Leads to Questioning Their Origins 7 Lens Specimen mount Screw plate Focusing screw Elevating screw (A) (B) (C) FIGURE 1.2 Viewing Animalcules. (A) To view his animalcules, Leeuwenhoek placed his sample on the tip of the specimen mount that was attached to a screw plate. An elevating screw moved the specimen up or down, whereas the focusing screw pushed against the metal plate, moving the specimen toward or away from the lens. (B) Holding the microscope up to the bright light, Leeuwenhoek then looked through the lens to view his sample. (C) From such observations, Leeuwenhoek drew the animalcules he saw (bacteria in this drawing). »» Why would Leeuwenhoek believe his living (and often moving) creatures were tiny animals? (B) Collection of the University of Michigan Health System, Gift of Pfizer, Inc. (UMHS.15). (C) © Royal Society, London. Aware of Hooke’s Micrographia, Leeuwenhoek at the time found it difficult to repeat and verify his turned his microscope to the invisible world. Begin- observations, which also are key components of sci- ning in 1673 and lasting until his death in 1723, entific inquiry. Still, Leeuwenhoek s observations of Leeuwenhoek communicated his microscope obser- animalcules opened yet a second door to another vations through more than 300 letters to England’s entirely new world: the world of the microbe. Royal Society. In 1674, one of his first letters described a sample of lake water. Placing the sample before his Do Animalcules Arise Spontaneously? lens, he described hundreds of tiny, moving particles In the early 1600s, most naturalists were vitalists, he thought were minute, living animals, which he individuals who thought life depended on a myste- called animalcules. In fact, this discovery represents rious and pervasive “vital force” in the air. This force one of the most important observations in history provided the basis for the doctrine of spontaneous because Leeuwenhoek had described and illustrated generation, which suggested that some forms of life for the first time the microbial world. In 1676, he could arise from nonliving, often decaying matter. mixed pepper with a previously collected sample of Others also embraced the idea, for they too wit- snow water. After three weeks, he found more animal- nessed toads that appeared from mud, snakes com- cules, including the first unmistakable observations ing from the marrow of a decaying human spine, of bacteria (FIGURE 1.2C). Among the other letters and rats arising from garbage wrapped in rags. sent to the Royal Society, he described all the differ- Resolving the reality of such bizarre beliefs ent types of microbes (except viruses) that we know would require a new form of investigation— of today. This included structural details of yeast cells, experimentation—and a new generation of experi- thread-like fungi, and microscopic algae and protozoa. mental naturalists arose. The process of “observation” is an important skill for all scientists and remains the cornerstone of all scientific inquiry. ooke and Leeuwenhoek Redi’s Experiments are excellent examples of individuals with sound In 1668, the Italian naturalist Francesco Redi per- observational skills. nfortunately, Leeuwenhoek formed one of history s first biological e periments. invited no one to work with him, nor did he show As described in INVESTIGATING THE MICROBIAL anyone how he made his lenses. Thus, naturalists WORLD 1, his experiment was designed to test the 8 CHAPTER 1 MICROBIOLOGY: THEN AND NOW Investigating the Microbial World 1 Can Life Arise Spontaneously? For centuries, many people, learned and not, believed that some forms of life could arise spontaneously from nonliving, decaying matter. For example: OBSERVATION: In the 17th century, many people believed that fly maggots (larvae) arose spontaneously from rotting meat. Francesco Redi set out to find the answer. QUESTION: Do fly maggots arise spontaneously from rotting meat? HYPOTHESIS: Redi proposed that fly maggots arise from hatched eggs laid in decaying meat by flies. If so, preventing flies from laying eggs in the rotting meat should result in no maggots being generated. EXPERIMENTAL DESIGN: Redi obtained similar pieces of rotting meat and jars in which the meat would be placed. EXPERIMENT: One piece of meat was placed in an open jar, whereas the other piece was placed in a similar jar that was then covered with a piece of gauze to keep out any flying insects, including flies. The meat in each jar was allowed to rot. RESULTS: See figure. Open jar Covered jar Rotting allowed to occur Open jar Covered jar CONCLUSIONS: QUESTION 1: From Redi’s experiments, was his hypothesis validated? Explain using the figure. QUESTION 2: What is the control in this experiment, and why was it important to have a control? QUESTION 3: Why was it important that Redi used gauze to cover the one jar and not seal it completely? Hint: Remember what people believed about the “vital force.” You can find answers in Appendix E. Modified from Redi, F. 1688. As reprinted by Open Court Publishing Company, Chicago (1909).  KEY CONCEPT 1.1 The Discovery of Microbes Leads to Questioning Their Origins 9 belief that worm like maggots y larvae could conclusions and suggested that the animalcules arise spontaneously from rotting meat. came from the air and would therefore grow in the Although Redi s e periments verified that spon- broth of the cooled asks. To validate his claim, in taneous generation did not produce larger living 1765, he repeated Needham’s experiments by boil- creatures like maggots, what about the mysteri- ing asks with broth for an e tended time before ous and microscopic animalcules that appeared to sealing some asks. After 2 days, the broths in straddle the boundary between the nonliving and the open asks were swarming with animalcules, living world Could they arise spontaneously whereas the sealed ones contained no animalcules. Spallanzani concluded that microbes from the air, Needham’s Experiments and not spontaneous generation, accounted for the presence of animalcules in the asks. In 1745, a British clergyman and naturalist, John The controversy over spontaneous generation of Needham, proposed that the spontaneous genera- animalcules continued into the mid-1800s and only tion of animalcules resulted from a vital force that deepened when Rudolf Virchow, a erman patholo- reorganized decaying matter into life. Needham pre- gist, put forward, without direct evidence, the idea sented experiments showing that animalcules could of biogenesis, which said that life arises only from arise spontaneously in asks of animal broth that life. To solve the debate concerning microbial spon- previously had been heated and then kept at room taneous generation, a new experimental strategy temperature for several days. He was convinced that would be needed. the vital force provided the stimulus needed for spontaneous generation. Pasteur’s Experiments Louis Pasteur, a French chemist and scientist, took Spallanzani’s Experiments up the challenge of spontaneous generation, and in Experiments often can be subject to varying inter- 1861 he designed an elegant series of experiments pretations. As such, the Italian cleric and natu- that were a variation of the methods of Needham ralist Lazzaro Spallanzani challenged Needham s and Spallanzani. The box MICROINQUIRY 1 outlines MICROINQUIRY 1 Scientific Inquiry and Spontaneous Generation Science is a systematic way of thinking and learning about that organisms do not appear from nonliving matter but the natural world. Often we accept and integrate into our rather from the air in which they are located. understanding new information because it appears con- Question: Next comes the question, which can be asked sistent with what we believe is true. But, are we sure our in many ways but usually as a “what,” “why,” or “how” ideas are always correct? In science, scientific in uiry, or question. For example, “What accounts for the generation what has been called the “scientific method,” is a way to of microorganisms in the animal broth?” examine those ideas. Hypothesis: A hypothesis is a provisional but testable Scientific inquiry often uses deductive reasoning, which explanation for an observed phenomenon or observation. begins with general observations, builds a hypothesis, Pasteur’s hypothesis was that “Organisms appearing in carries out well-designed and carefully executed exper- the sterile flask come from other organisms in the air.” If iments to test the hypothesis, and reaches a specific, so, air allowed to enter the sterile flask will contain organ- logical conclusion. Pasteur used this inquiry approach in isms that will grow in such profusion that they will be 1861 to test the idea of spontaneous generation of micro- seen as a cloudy liquid. organisms. Let’s see how it worked: Let’s analyze the experiments. In Pasteur’s experimen- Observations: When studying a problem, the inquiry tal design, only one variable (an adjustable condition) process usually begins with observations. For spontane- changed. In the accompanying figure, one flask remained ous generation, Pasteur’s earlier observations suggested intact, whereas two others were exposed to the air by (continues) 10 CHAPTER 1 MICROBIOLOGY: THEN AND NOW MICROINQUIRY 1 (Continued) Scientific Inquiry and Spontaneous Generation (A) breaking the neck or (B) tipping the flask. Pasteur kept appeared in the intact flask is interesting but tells us very all other factors the same; that is, all of the broths were little by itself. Its significance comes by comparing it to heated and cooled for the same length of time, and the the broken neck flask and tipped flask where organisms flasks were identical. Thus, the experiments had a rigor- quickly appeared. ous control (the comparative condition wherein the flask Conclusion: Pasteur’s hypothesis was supported by the remained intact). Pasteur’s finding that no organisms experiments. General When studying a problem, the inquiry process usually begins with observations. For spontaneous generation, observations Pasteur’s earlier observations suggested that organisms do not appear from nonliving matter but rather from the air in which they are located. Question Next comes the question, which can be asked in many ways but usually as a “what,” “why,” or “how” question. For example, “What accounts for the appearance of microorganisms in the animal broth?” Hypothesis A hypothesis is a provisional but testable explanation for the question or observation. Pasteur’s hypothesis was that “Organisms appearing in the sterile flask come from other organisms in the air.” If so, then air allowed to enter the sterile flask will contain organisms that will grow in such profusion that they will be seen as a cloudy liquid. Swan-necked flask Experiments Dust and microorganisms Air Flask Time are trapped cooled passes enters Sterile broth No organisms The experiment appear begins with a boiled (A) (B) broth solution similar Flask neck Flask tilted so to that of Needham snapped off broth enters neck Time and Spallanzani. passes Specific results Organisms appear Organisms appear Conclusions Pasteur and the Spontaneous Generation Controversy. If broth sterilized in a swan-necked flask is left open to the air, the curvature of the neck traps dust particles and microorganisms, preventing them from reaching the broth. However, if the neck is snapped off to allow in air or the flask is tipped so broth enters the neck, organisms encounter the broth and grow. the process of scientific inquiry and Pasteur s in spontaneous generation and validated the idea of experiments. biogenesis. Although Pasteur’s experiments generated con- Today there is another form of “spontaneous siderable debate for several years, his exacting and generation” occurring—this time in the research carefully designed experiments disproved the belief laboratory, as MICROFOCUS 1.1 relates.  KEY CONCEPT 1.2 Disease Transmission Can Be Prevented 11 MICROFOCUS 1.1: Biotechnology Generating Life—Today Those who believed in spontaneous generation proposed that animalcules arose from the rearrangement of molecules released from decayed organisms. Although this idea for the generation of life was incorrect, today we are getting closer to generating new life by rearranging molecules in the laboratory. In 2002, scientists at the State University of New York, Stony Brook, reconstructed a poliovirus by assembling separate poliovirus genes and proteins. A year later, Craig Venter and his group assembled a bacteriophage—a virus that infects bacterial cells—from “off-the-shelf” biomolecules. Then, in 2010, another team, again led by Venter, synthesized from scratch the complete genetic sequence of the bacterium Mycoplasma mycoides and inserted the sequence into a cell of Mycoplasma capricolum from which its genetic information previously had been removed (see figure). This “new organism” now functioned like an M. mycoides cell. However, this is not “generating new life.” Rather, it is putting a new set of genes into another cell that never before had that set of genes. This new field of biology is called synthetic biology, and it aims to rebuild or create new “life forms” (such as bacterial cells) from scratch by recombining molecules taken from other organisms. It is like fashioning a new car by taking various parts from a Ford and Chevy and assembling them on a Toyota chassis. Why do this? The design and construction of novel organisms, having functions very different from naturally occurring organisms, present the opportunity to expand evolution’s repertoire by fabricating cells that are better at doing specific jobs. Can we, for example, design bacterial cells that are better at degrading toxic wastes, providing alternative energy sources, or making cheaper pharmaceuticals? These and many A false-color electron microscope image of synthetic other positive benefits are envisioned as outcomes of synthetic Mycoplasma cells. (Bar = 1 μm.) biology and the generation of new life. © Thomas Deerinck, NCMIR/Science Source. Concept and Reasoning Checks 1.1 a. How were the first microbes discovered? b. If you were alive in Leeuwenhoek’s time, how would you explain the origin for the animalcules he saw with his simple microscope? c. Evaluate the role of experimentation as an important skill to the eventual rejection of spontaneous generation as an origin for animalcules (and microbes). KEY CONCEPT 1.2 Disease Transmission Can Be Prevented In the 13th century, people knew diseases could be contagious, disfiguring, and often deadly disease that transmitted between individuals, so they enforced affected humans. In an effort to prevent individuals isolations, called quarantines, in an attempt to pre- from contracting smallpox, the Chinese practiced vent disease spread. Other interventions to prevent variolation, which involved blowing a ground small- infection can be traced back to the 14th century. At pox powder into the nose of individuals. By the 18th that time, and throughout history, smallpox was a century, Europeans were inoculating dried smallpox 12 CHAPTER 1 MICROBIOLOGY: THEN AND NOW scabs under the skin of the arm. Although some individuals did get smallpox, most contracted only Leather hat (indicating a mild form of the disease and, upon recovery, were a doctor) protected against subsequent smallpox exposures. Mask with glass eyes and beak containing a Vaccination Prevents the Spread of Smallpox “protective” perfumed sponge In the late 1700s, smallpox epidemics were preva- lent throughout Europe. In England, smallpox epi- Stick to remove clothes demics were so severe that one-third of the children of a plague victim died before the age of three and many victims who recovered often were blinded and left pockmarked. Gloves As an English country surgeon, Edward Jenner learned that milkmaids who occasionally contracted Waxed linen robe a mild disease called cowpox would subsequently be protected from contracting smallpox. Because cow- Boots pox was not deadly, Jenner hypothesized that inten- tionally giving cowpox to people should protect them against smallpox. In 1796, he took a scraping of a cowpox blister from a milkmaid’s hand and FIGURE 1.3 Dressed for Protection. This dress was scratched it into the skin of a young boy’s arm. The thought to protect a plague doctor from the air (miasma) that caused the plague. »» How would each item of dress offer boy soon developed a slight fever but recovered. Six protection? weeks later, Jenner infected the boy with smallpox pus. Within days, the boy developed a reaction at Courtesy of National Library of Medicine. the skin site but failed to show any sign of smallpox. In 1798, Jenner repeated his experiments with poisonous particles of rotting matter expelled into others, verifying his technique of vaccination (vacca the air (the word “malaria” comes from mala aria, “cow”. Prominent physicians soon confirmed his meaning “bad air”). To protect oneself from the findings, and within a few years, Jenner s method black plague, for example, plague doctors in Europe of vaccination spread through Europe and abroad. often wore an elaborate costume they thought would However, it would not be until 1980, some 284 years protect them from the plague miasma (FIGURE 1.3). after Jenner s first smallpo vaccinations, that the As the 19th century unfolded, more scientists World Health Organization (WHO) would certify were relying on keen observations and experimenta- that smallpox had been eradicated globally through tion as a way of understanding and explaining disease a massive vaccination effort that was carried out transmission—and challenging the idea of miasmas. between 1966 and 1979. Epidemiology, as applied to infectious diseases, In retrospect, it is remarkable that without any is another e ample of scientific inquiry—in this case knowledge of microbes or disease causation, Jenner to identify the source, cause, and mode of trans- accomplished what he did. Again, hallmarks of a mission of disease within populations. The first scientist—keen observational skills and insight—led such epidemiological studies, carried out by Ignaz to a therapeutic intervention against disease. His Semmelweis and John Snow, were instrumental in work, along with others, would lay the foundation suggesting how diseases were transmitted and how for the field of immunology, the study of the body’s simple measures could prevent transmission. defenses against, and responses to, foreign organ- isms and substances. Semmelweis and “Cadaver Matter” Ignaz Semmelweis was a Hungarian obstetrician Disease Transmission Does Not Result from who, at the age of 29, was appointed chief resi- a Miasma dent at a large maternity hospital in Vienna, Aus- So, the question remains. What causes infectious tria. Soon after his arrival, he was shocked by the disease In the 1700s, the prevalent belief among numbers of women in his ward who were dying of naturalists and laypersons alike was that disease childbed fever (a type of blood poisoning also called resulted from a miasma, which was thought to arise puerperal fever) following labor. The box CLINICAL from a foul quality of the atmosphere or from tiny CASE 1 outlines Semmelweis’ investigations into  KEY CONCEPT 1.2 Disease Transmission Can Be Prevented 13 Clinical Case 1 Childbed Fever: A Historical Reflection In 1844–1846, many mothers in 20 the First Maternity Division of the Vienna hospital first maternity division Vienna General Hospital, which was Vienna hospital second maternity division run by doctors and medical students, contracted a serious disease called childbed fever (puerperal fever). Up 15 Percent Deaths, Childbed Fever to 11% of the mothers died from the illness. However, in the adjacent Second Maternity Division of the same hospital run by midwives, the death toll from childbed fever was 10 less than 3% over the same period. As a member of the medical staff of the First Division, Ignaz Semmelweis searched for an explanation for the high mortality in his division. 5 Most of the medical staff attributed the illnesses and deaths of puerperal fever to an unavoidable miasma. 0 Semmelweis discounted this belief because how could one reconcile the 00 02 04 06 08 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 fact that while the fever was raging in the First Division, few cases occurred Yearly Mortality for Childbed Fever 1800–1849. Semmelweis collected data in the Second Division, and hardly a on deaths of birthgiving mothers in the Vienna maternity hospital (red line) and case occurred in the surrounding city compared the deaths to those in the second maternity division where midwives of Vienna? focused on attending to births and did not concern themselves with anatomical Others attributed the fever to pathology. »» Why do Semmelweis’ observations on the prevalence of childbed fever overcrowding in the First Division. not support a miasma as the cause of and transmission for the disease? Semmelweis pointed out that, in Data from Semmelweis (1861). fact, the crowding was heavier in the Second Division. In addition, there were no differences between the two divisions with regard to diet, general care, and method of examination of maternity patients. In 1847, Jakob Kolletschka, professor of forensic medicine in the hospital and a colleague of Semmelweis, was instructing medical students in the art of medical dissection of cadavers in the morgue (deadhouse). While performing an autopsy, Kolletschka punctured a finger with a bloody scalpel. He ended up dying from the infection and Semmelweis observed that Kolletschka exhibited the same symptoms as the victims of childbed fever. Semmelweis also noted that (a) in the Second Division, the midwives neither received anatomical instruction nor did they dissect cadavers in the deadhouse; (b) he and his medical students examined women in labor in the First Division without cleaning up after performing their dissections in the deadhouse (see figure). Questions: a. How was the childbed fever illness transmitted to Professor Kolletschka? b. From Semmelweis’ observations, what was the source of childbed fever? c. Why was the incidence of the disease so low in the Second Division? d. How was the agent of childbed fever transmitted to maternity patients in the First Division? You can find answers in Appendix E. For additional information, read The Doctors’ Plague: Germs, Childbed Fever, and the Strange Story of Ignác Semmelweis by Sherwin B. Nuland. (New York: W.W. Norton & Company. 2004.) 14 CHAPTER 1 MICROBIOLOGY: THEN AND NOW the source and mode of transmission of the dis- ease and the intervention he introduced to stop the transmission of childbed fever. After Semmelweis directed his staff to wash their hands in chlorine water before entering the maternity ward, deaths from childbed fever imme- diately plummeted. Semmelweis believed “cadaver matter” on the hands of the staff doctors was the agent of disease and its transmission could be inter- rupted by hand washing. nfortunately, few physi- cians initially heeded Semmelweis’ measures and he was relieved of his position in 1849. It is believed Content removed due to copyright restrictions that he might have died in 1865 from the very infec- tious agent he had studied. Snow and “Organized Particles” In 1854, a cholera epidemic hit London s Soho district. With many residents dying, English sur- geon John Snow carried out one of the first thor- ough epidemiological studies to discover how this acute intestinal infection was spread. By inter- viewing sick and healthy Londoners and plotting the location of each cholera case on a district map (FIGURE 1.4), Snow discovered that most chol- era cases were linked to a sewage-contaminated FIGURE 1.4 Blocking Disease Transmission. John Snow (inset) produced a map plotting all the cholera cases (black water pump on Broad Street from which numer- rectangles) in the London Soho district and observed a cluster ous local residents obtained their household (circle) near the Broad Street pump (red arrow). »» Why would drinking water. removing the pump handle stop the spread of cholera? Although Snow did not know the cause of chol- era, he hypothesized that the Broad Street water pump was the source of the infectious agent. Snow instituted the first known e ample of a public health measure to prevent disease transmission—he requested the parish Board of uardians to remove The Stage Is Set the handle from the Broad Street pump Cholera During the early years of the 1800s, other events cases dropped and again disease spread was broken occurred that helped set the stage for the coming by a simple procedure. “germ revolution.” In the 1830s, advances were Similar to Semmelweis’ cadaver matter, Snow made in microscope optics that allowed better res- believed “organized particles” in the water caused olution of objects. This resulted in improved and cholera; this was another hypothesis that proved to more widespread observations of tiny living organ- be correct even though the causative agent would isms, many of which resembled short sticks. In fact, not be identified for another 29 years. in 1838 the erman biologist Christian hrenberg It is important to realize that although the suggested these “rod-like” looking organisms be miasma premise was incorrect, the fact that dis- called bacteria (bakter = “rod”). ease was associated with bad air and filth led to new To understand clearly the nature of infectious hygiene measures, such as cleaning streets, laying disease, a new concept of disease had to emerge. In new sewer lines in cities, and improving working doing so, it would be necessary to demonstrate that conditions. These changes helped usher in the San- a specific infectious disease was caused by a specific itary Movement and create the infrastructure for “germ.” This would require some very insightful the public health systems we have today, which is a work, guided by Louis Pasteur in France and Robert team effort explained in MICROFOCUS 1.2. och in ermany.  KEY CONCEPT 1.2 Disease Transmission Can Be Prevented 15 MICROFOCUS 1.2: Public Health Epidemiology—Today On September 2, 2011, the Colorado Department of Public Health and Environment reported an abnormally high number of people admitted to local hospitals suffering from fever and muscle aches as well as diarrhea or other gastrointestinal symptoms. Doctors quickly diagnosed the illness as a bacterial infection caused by Listeria monocytogenes. In the footsteps of Semmelweis and Snow, today’s health experts needed to locate rapidly the source and transmission mechanism of this outbreak. This often requires an entire team of medical investigators, including those from the Centers for Disease Control and Prevention (CDC), state and local health departments, and the Coordinated Outbreak Response and Evaluation (CORE) Network, which is part of the Food and Drug Administration (FDA). See figure. For this outbreak, the CORE team was made up of epidemiologists, microbiologists, health specialists, consumer safety officers, and policy analysts. The CORE surveillance team confirmed that Listeria was the infectious agent, while the response team identified locally grown Listeria-contaminated whole cantaloupes as the source of the outbreak. They then issued a national warning, as the number of cases had expanded beyond Colorado. After the outbreak, the CORE post-response team discovered that the farm growing the cantaloupes had failed to follow safe food-handling practices in the facility where the whole cantaloupes were stored and packed for shipment. The farm also failed to adequately clean the processing equipment, which had been used incorrectly, leading to the contamination. Even with this rapid response, the Listeria cantaloupe contamination was the deadliest foodborne disease outbreak in the United States in nearly 90 years, killing 30 people and sickening 146 in 28 states. Unlike the time of Semmelweis and Snow, today’s potential for disease spread requires numerous response teams with the expertise and know- how like CORE. With an ever-present danger of emerging A group of FDA medical investigators form a Coordinated disease, epidemiology today is a team effort that remains a Outbreak Response and Evaluation (CORE) team. critical tool in the fight against infectious disease. Courtesy of FDA. Concept and Reasoning Checks 1.2 a. How do the procedures of variolation and vaccination contradict the concept of miasmas? b. How did the work of Semmelweis and Snow challenge the widely held idea of miasmas as the cause of infectious disease? Chapter Challenge A We are beginning to see how microbes and pathogens were discovered through the observations and studies of natural philosophers, a vaccine pioneer, and the first epidemiologists. QUESTION A: What three infectious diseases described in this section were thought to be caused by a miasma? What types of studies and actions suggested these diseases were not the product of a miasma? You can find the answers in Appendix F. 16 CHAPTER 1 MICROBIOLOGY: THEN AND NOW KEY CONCEPT 1.3 The Classical Golden Age of Microbiology Reveals the Germ Beginning around 1854, the association of microbes alcohol. Fermentation, then, was a biological process with the disease process blossomed. Over the next and yeasts were living agents responsible for fer- 60 years, the foundations would be laid for the mentation. maturing process that has led to the modern sci- Pasteur also demonstrated that wines, beers, and ence of microbiology. This period is referred to as vinegar each contained different and specific types the first, or classical, olden Age of microbiology. of microorganisms that had specific properties. For example, in studying a local problem of wine souring, Louis Pasteur Proposes That Germs Cause he observed that only the soured wines contained Infectious Disease populations of bacterial cells (FIGURE 1.5B). Pasteur Trained as a chemist, Louis Pasteur FIGURE 1.5A) concluded that these cells must have contaminated was among the first scientists who believed that a batch of yeast and, as another example of a bio- problems in science could be solved in the labora- logical process, produced the acids that caused the tory with the results having practical applications. souring. Pasteur recommended a practical solution Always one to tackle big problems, Pasteur soon for the “wine disease” problem: heat the wine gently set out to understand the chemical process of fer- to kill the harmful bacterial cells but not so strongly mentation. The prevailing theory in the 1850s held as to affect the quality of the wine. His controlled that fermentation was strictly a chemical process heating technique, which would become known as and the yeasts needed for fermentation were sim- pasteurization, soon was applied to other products. ply inert chemical “globules” catalyzing the pro- Today, pasteurization is a universal method used to cess. Pasteur’s microscope observations, however, kill pathogens and retard spoilage in milk and many consistently revealed large numbers of tiny yeast other foods and beverages. cells in fermented juice. When he mixed yeast If wine disease was caused by tiny, living bacte- in a sugar-water solution in the absence of air, ria, Pasteur reasoned that human infections and dis- the yeast multiplied and converted the sugar to ease also might be caused by other microorganisms (A) (B) FIGURE 1.5 Louis Pasteur and Fermentation Bacteria. (A) Louis Pasteur as a 46-year-old professor of chemistry at the Uni- versity of Paris. (B) A drawing of some of the bacterial cells Pasteur observed in soured wine. »» Why would such cells exist in a wine bottle that had soured? Courtesy of National Library of Medicine.  KEY CONCEPT 1.3 The Classical Golden Age of Microbiology Reveals the Germ 17 in the environment—what he called germs. Thus, Therefore, germs can come from the environment— Pasteur formulated the germ theory of disease, and they can be controlled. which held that some microorganisms are respon- sible for infectious disease. Silkworm Disease and Cholera The Work of Lister and Pasteur Stimulate Between 1857 and 1878, Pasteur sought more evi- Disease Control and Reinforce dence for his germ theory idea. In 1865, Pasteur the Germ Theory had the opportunity to study pébrine, an infectious disease of silkworms. After several setbacks and Pasteur had reasoned that if germs were acquired 5 years of work, he finally identified a new type of from the environment, their spread could be con- germ, unlike the bacterial cells and yeast he had trolled and the chain of disease transmission bro- observed with his microscope. These tiny germs, ken, as Semmelweis and Snow had shown years which he called “corpuscular parasites”, were the earlier. infectious agent in silkworms and on the mulberry leaves fed to the worms. By separating the healthy Lister and Antisepsis silkworms from the diseased silkworms and their earing of Pasteur s germ theory, Joseph Lister, a contaminated food, he managed to quell the spread professor of surgery at lasgow Royal Infirmary in of the silkworm disease. The identification of the Scotland, wondered if germs were responsible for pathogen was crucial to supporting the germ the- the large number of postoperative infections among ory, and Pasteur would never again doubt the ability his amputation patients. So, in 1865, knowing that of germs to cause infectious disease. carbolic acid had been effective on sewage control, Also in 1865, cholera engulfed Paris, killing 200 Lister used a carbolic acid spray in surgery and on people a day. Determined to find the causative agent, surgical wounds (FIGURE 1.6). The results were Pasteur tried to capture the responsible germ by fil- spectacular—the wounds healed without infection tering the air around hospitalized patients and trap- in almost 70% of his cases. His technique would ping the germs in cotton. nfortunately, Pasteur soon not only revolutionize medicine and the could not grow or separate one type of germ from oth- practice of surgery but also lead to the practice of ers because his broth cultures allowed all the organ- antisepsis, the use of chemical methods for disin- isms on the cotton to mix freely. To validate the germ fection of external living surfaces, such as the skin. theory, what was missing was the ability to isolate a FIGURE 1.6 Lister and Antisepsis. Joseph Lister (inset) and his students used a carbolic acid spray in surgery and on surgi- cal wounds to prevent postoperative infections. »» Hypothesize how carbolic acid prevented surgical infections. Mary Evans Picture Library/Alamy Images. Inset courtesy of National Library of Medicine.  18 CHAPTER 1 MICROBIOLOGY: THEN AND NOW specific germ from a diseased individual and demon- took several spores on a sliver of wood and injected strate the isolated germ caused that same disease. them into healthy mice. The signs of anthrax soon appeared, and when Koch autopsied the animals, he found their blood swarming with the same type Robert Koch Formalizes Standards to of bacterial cells. ere was the first evidence that a Equate Germs with Infectious Disease specific germ was the causative agent of a specific Robert och FIGURE 1.7A was a erman country disease. doctor who was well aware of anthrax, a deadly dis- Koch found that growing bacterial cells was not ease that periodically ravaged cattle and sheep and very convenient. Then, in 1880, he observed a slice of also could cause disease in humans. Was anthrax potato on which small masses of bacterial cells, which caused by a germ he termed colonies, were multiplying in number. Koch In 1875, Koch injected mice with the blood from tried adding gelatin to his broth to prepare a similar sheep suffering anthrax. He noticed the mice soon solid culture surface. He then inoculated bacterial developed the same disease signs seen in the sheep. cells on the surface and set the dish aside to incubate. Next, he isolated a few rod-shaped bacterial cells Within 24 hours, visible colonies were growing on from the blood and, with his microscope, watched for the surface, each colony representing a pure culture hours as the bacterial cells multiplied, formed tan- containing only one bacterial type. By 1884, a poly- gled threads, and finally reverted to spores. e then saccharide called agar that was derived from marine Postulate 1 The same microorganisms are present in every case of the disease. Anthrax bacilli Spore Postulate 2 The microorganisms are isolated from the tissues of a dead animal, and a pure culture is prepared. Postulate 4 The identical micro- organisms are isolated and recultivated from the tissue specimens of the experimental animal. Postulate 3 Microorganisms from the pure culture are inoculated into a healthy, susceptible animal. The disease is reproduced. (B) (A) FIGURE 1.7 A Demonstration of Koch’s Postulates. Robert Koch (A) developed what became known as Koch’s postulates (B) that were used to relate a single microorganism to a single disease. The inset (in the upper right) is a photo of the rod- shaped anthrax bacterial cells. Many rods are swollen with spores (white ovals). »» What is the relationship between postulate 2 and postulate 4? (A) Courtesy of National Library of Medicine. (B) Inset courtesy of the CDC.  KEY CONCEPT 1.3 The Classical Golden Age of Microbiology Reveals the Germ 19 MICROFOCUS 1.3: History Jams, Jellies, and Microorganisms 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 room temperature and produced discrete, visible colonies. On occasion, however, Koch was dismayed to find that the gelatin turned to liquid because some bacterial species produced a chemical substance that digested the gelatin. Moreover, gelatin liquefied at the warm incubator temperatures commonly used to cultivate many bacterial species. An associate of Koch’s, Walther Hesse, mentioned the problem to his wife and laboratory assistant, Fanny Hesse. She had a possible solution. For years, she had been using a seaweed-derived powder called agar (pronounced ah’gar) to solidify her jams and jellies. Agar was valuable because it mixed easily with most liquids and once gelled, it did not liquefy, even at warm incubator temperatures. In 1880, Walther Hesse recommend agar to Koch. Soon Koch was using it routinely to grow bacterial species, and, in 1884, he first mentioned agar in his paper on the isolation of the bacterial organism responsible for tuberculosis. It is noteworthy that Fanny Hesse is one of the first Americans (she was originally from New Jersey) to make a significant contribution to microbiology. Fanny Hesse. Another key development, the common petri dish (plate), also was invented Courtesy of National Library of Medicine. about this time (1887) by Julius Petri, one of Koch’s former assistants. algae replaced gelatin as Koch’s preferred solidifying for tuberculosis and cholera. In addition, many agent, as MICROFOCUS 1.3 recounts. other individuals quickly discovered other germs When Koch presented his work, scientists were causing other human diseases (TABLE 1.1). Pas- astonished. ere was the verification of the germ teur’s lab, on the other hand, was more concerned theory that had eluded Pasteur. Koch’s procedures with preventing disease through vaccination. This became known as Koch’s postulates and were culminated in 1885, when Pasteur’s rabies vaccine quickly adopted as the formalized standards for saved the life of a young boy who had been bitten implicating a specific germ with a specific disease. by a rabid dog. By the turn of the century, the germ FIGURE 1.7B outlines the four-step process. theory set a new course for studying and treating By applying och s postulates, germ identifica- infectious disease. The detailed studies carried out tion in the laboratory became the normal method of by Pasteur and Koch made the discipline of bacte- work. Koch’s lab focused on disease causation (eti- riology, the study of bacterial organisms, a well- ology), including the bacterial agents responsible respected field of study. Concept and Reasoning Checks 1.3 a. How did Pasteur’s studies of wine fermentation and souring suggest to him that germs might cause human infectious disease? b. Assess Lister’s antisepsis procedures and Pasteur’s studies of pébrine to supporting the germ theory. c. Explain why Koch’s postulates were critical to validating the germ theory. d. How did the development of pure cultures advance the germ theory? 20 CHAPTER 1 MICROBIOLOGY: THEN AND NOW TABLE 1.1 ther International Scientists Who Identified Specific uman athogens During the Classical Golden Age of Microbiology Investigator (Year) Country Disease (Pathogenic Agent) Otto Obermeier (1868) Germany Relapsing fever (bacterium) Gerhard Hansen (1873) Norway Leprosy (bacterium) Albert Neisser (1879) Germany Gonorrhea (bacterium) Charles Laveran (1880) France Malaria (protozoan) Karl Eberth (1880) Germany Typhoid fever (bacterium) Edwin Klebs (1883) Germany Diphtheria (bacterium) Arthur Nicolaier (1884) Germany Tetanus (bacterium) Theodore Escherich (1885) Germany Infant diarrhea (bacterium) Albert Fraenkel (1886) Germany Pneumonia (bacterium) David Bruce (1887) Australia Undulant fever (bacterium) Anton Weichselbaum (1887) Austria Cerebrospinal meningitis (bacterium) A. A. Gärtner (1888) Germany Food poisoning/salmonellosis (bacterium) William Welch and George United States Gas gangrene (bacterium) Nuttall (1892) S. Kitasato and A. Yersin (1894) Japan and France (Independently) Bubonic plague (bacterium) Emile van Ermengem (1896) Belgium Botulism (bacterium) Kiyoshi Shiga (1898) Japan Bacterial dysentery (bacterium) Walter Reed (1900) United States Yellow fever (virus) Robert Forde and Joseph Everett Great Britain African sleeping sickness Dutton (1902) (protozoan) Fritz Schaudinn and Erich Germany Syphilis (bacterium) Hoffman (1903) Jules Bordet and Octave France Whooping cough/pertussis Gengou (1906) (bacterium) George McCoy and Charles United States Tularemia (bacterium) Chapin (1911)  KEY CONCEPT 1.4 With the Discovery of Other Microbes, the Microbial World Expands 21 KEY CONCEPT 1.4 With the Discovery of Other Microbes, the Microbial World Expands Although bacterial organisms were being discovered first seen by Leeuwenhoek was another ma or as the agents of some human diseases, why couldn’t milestone in understanding infectious disease. In och s postulate confirm a bacterial origin for dis- fact, Pasteur’s “corpuscular parasites” of pébrine eases such as measles, mumps, smallpox, and yellow were protozoa. Other advances in the study of these fever Moreover, what were the bacterial organisms types of microbes were dependent on studies in being discovered in the soil doing tropical medicine. Ma or advances in understand- ing these microbes included Charles Laveran s dis- Other Global Pioneers Contribute to the New covery (1880) that the protozoan parasite causing Discipline of Microbiology malaria could be found in human blood and David Bruce’s studies (1887) that another protozoan par- In the 1890s, a Russian scientist, Dimitri Ivanowsky, asite was the agent of human sleeping sickness. and Martinus Bei erinck, a Dutch investigator, With these studies, the field of protozoology was independently were studying tobacco mosaic dis- born (FIGURE 1.8). ease, which produces mottled and stunted tobacco As you should now know, not all microbes leaves. Each independently prepared a homoge- are pathogens; in fact, as described in the chap- nized liquid from diseased plants in the hopes of ter opener, relatively few cause infectious disease. trapping the infectious agent on the filter. In fact, Consequently, during the first olden Age of micro- they discovered that when the liquid that passed biology, other scientists and microbiologists were through a filter was applied to healthy tobacco keenly interested in microbes naturally found in the plants, the leaves became mottled and stunted. soil, and they wanted to understand the ecological Ivanowsky simply assumed bacterial cells somehow importance of these nonpathogenic microbes. The had slipped through the filter, whereas Bei erinck Russian soil scientist Sergei Winogradsky, a stu- suggested that the liquid was a “contagious, liv- dent of de Bary s, and Martinus Bei erinck discov- ing liquid” that acted like a poison or virus (virus = ered that some bacterial organisms could convert “poison”). Then, in 1898, the causative agent for inert atmospheric nitrogen gas (N2) into biolog- animal hoof-and-mouth disease was found to be ically useable ammonia (NH3) that plants need. another filterable liquid, and, in 1901, American Winogradsky and Beijerinck each developed many Walter Reed, a nited States Army physician, con- of the laboratory methods essential to the study of cluded that the agent responsible for yellow fever soil microbes, while uncovering the essential roles in humans also was a virus. With these discoveries, such microorganisms play in the recycling of mat- the discipline of virology, the study of viruses, was ter on a global scale. As the founders of microbial launched. ecology, Winogradsky and Beijerinck laid the foun- While scientists like Pasteur and Koch were dation for what we know today about many of the investigating the bacterial contribution to the so-called microbial workforce mentioned in the infectious disease process, others were identifying chapter opener. other types of disease-causing microbes. Fungi were Today, many microbiologists are still searching found to cause plant diseases and such diseases for, finding, and trying to understand the roles of were studied extensively by Anton de Bary in the microorganisms in the environment as well as in 1860s. As already mentioned in this chapter, Pas- health and disease. In fact, less than 2% of all micro- teur identified the role of fungal yeasts first seen by organisms on arth have been identified and many Leeuwenhoek with fermentation. Importantly, the fewer cultured, so there is still a lot to be discovered recognition that some fungi were linked to human and studied in the microbial world skin diseases was proposed as early as 1841 when a ungarian physician, David ruby, discovered a fungus associated with human scalp infections. The Microbial World Can Be Cataloged into These discoveries led to the development of the Unique Groups field of mycology, the study of fungi. As time went on, more and more microbes were The realization that infectious diseases could be identified and studied. Let s brie y survey what we caused by protozoa (again part of the animalcules know about these major groups of microorganisms. 22 CHAPTER 1 MICROBIOLOGY: THEN AND NOW MICROBIOLOGY studies Living Organisms Infectious Agents in the including disciplines of Bacteriology Mycology Parasitology Virology Virus-like Agents (multicellular) Phycology Protozoology FIGURE 1.8 Microbiology Disciplines. This simple concept map shows the relationship between microbiology and its various disciplines. Phycology is the study of algae and parasitology is the study of animal parasites, which traditionally includes the parasitic protozoa and the animal parasites (worms). Bacteria and Archaea springs), extremely salty (such as the Dead Sea), or of extremely low pH (such as acid mine drainage). It is estimated that there might be more than These so-called extremophiles evolved many adap- 10 million bacterial species. Most are very small, tations to survive in these extreme environments. single-celled (unicellular) organisms, although Conversely, many other archaeal organisms nor- some form filaments, and the ma ority associate in mally grow in temperate soils and water and are an a bacterial community called a “biofilm.” Almost integral part of the microbiome in animal digestive all bacterial cells have a rigid cell wall and many tracts. No archaeal members are known to be patho- common ones are spherical, spiral, or rod-shaped gens, but like the bacterial microbes, they are an (FIGURE 1.9A). They lack a cell nucleus and most of important part of Earth’s microbial workforce. the typical membrane-enclosed cellular compart- ments typical of other microbes and multicellular organisms. Many bacterial organisms get their food Viruses from the environment, although some make their Although not correctly labeled as microorganisms, own food through photosynthesis (FIGURE 1.9B). these “infectious agents” currently consist of more Bacterial cells are found in most all environments, than 100 million known types. Probably, most every making up, as previously mentioned, a large per- cell on Earth can be infected by some type of virus. centage of the Earth’s microbial workforce. Viruses are not cellular and cannot be grown in cul- In addition to the disease-causing members, some ture. They have a core of nucleic acid DNA or RNA are responsible for food spoilage, whereas others are surrounded by a protein coat. Among the features useful in the food industry. Many bacterial members, used to identify viruses are morphology (shape), along with several fungi, are decomposers, organisms genetic material DNA, RNA , and biological prop- that recycle nutrients from dead organisms. erties (the organism, tissue, or cell type infected). Based on recent biochemical and molecular stud- Viruses infect organisms for one reason only: ies, many bacterial organisms have been reassigned to replicate. Viruses in the air or water, for example, into another unique evolutionary group, called the cannot replicate because they need the metabolic Archaea. Although they look like bacterial cells machinery and chemical building blocks found inside when observed with the microscope, many of the living cells. Of the known viruses, only a small per- first members to be identified grew in environments centage cause disease in humans. Polio, the u, mea- that are extremely hot (such as the Yellowstone hot sles, AIDS, and smallpox are examples (FIGURE 1.9C).  KEY CONCEPT 1.4 With the Discovery of Other Microbes, the Microbial World Expands 23 (A) (B) (C) (D) (E) (F) FIGURE 1.9 Groups of Microorganisms. (A) A light microscope image of rod-shaped cells of Bacillus cereus (stained purple), a normal inhabitant of the soil. (Bar = 10 μm.) (B) A light microscope image of filamentous strands of Anabaena, a photosynthetic bacterium. (Bar = 100 μm.) (C) False-color electron microscope image of smallpox viruses. (Bar = 500 nm.) (D) A typical blue-gray Penicillium mold growing on a loaf of bread. (E) A light microscope image of the colonial green alga Volvox. (Bar = 300 μm.) (F) A light microscope image of the ribbon-like cells of the protist Trypanosoma, the causative agent of African sleeping sickness. (Bar = 10 μm.) »» Within these groups, why don’t organisms like Anabaena and Volvox cause disease? (A, B, E, F) Courtesy of Dr. Jeffrey Pommerville. (C) © Image Source Trading Ltd/Shutterstock. (D) © Jones & Bartlett Learning. Photographed by Kimberly Potvin. 24 CHAPTER 1 MICROBIOLOGY: THEN AND NOW The other groups of microbes have a cell nucleus impart distinctive avors in foods such as cheeses. and a variety of internal, membrane-bound cellular Together with many bacterial species, numerous compartments. molds play a major role as decomposers. Fungi Protists The fungi include the unicellular yeasts and the The protists consist mostly of protozoa and single- multicellular mushrooms and molds (FIGURE 1.9D). celled algae. Some are free living, whereas others About 100,000 species of fungi have been described; live in association with plants or animals. Move- however, there might be as many as 1.5 million spe- ment, if present, is achieved by agella or cilia or by cies in nature. a crawling motion. ther than some yeasts, molds grow as fila- Protists obtain nutrients in different ways. ments with rigid cell walls. Most grow best in warm, Some absorb nutrients from the surrounding envi- moist places and secrete digestive enzymes that ronment or ingest smaller microorganisms. The break down nutrients into smaller bits that can be unicellular, colonial, and filamentous algae have absorbed easily across the cell wall. Fungi, there- a rigid cell wall and can carry out photosynthesis fore, live in their own food supply. If that source of (FIGURE 1.9E). The aquatic protists also provide food is a human, diseases such as ringworm or vagi- energy and organic compounds for the lower trophic nal yeast infections can result. levels of the food web. Some protists (the protozoa) For the pharmaceutical industry, some fungi are capable of causing diseases in animals, includ- are sources for useful products, such as antibiot- ing humans; these include malaria, several types of ics. Others molds are used in the food industry to diarrhea, and sleeping sickness (FIGURE 1.9F). Concept and Reasoning Checks 1.4 a. Describe how viruses were discovered as disease-causing agents. b. What significant discoveries added the fungi and protozoa to the growing list of microbes? c. Judge the significance of the pioneering studies carried out by Winogradsky and Beijerinck. Chapter Challenge B By the end of the first Golden Age of microbiology (1915), all the major groups of microbes had been identified. QUESTION B: Construct a diagram or table that reveals how you could tell bacteria, viruses, fungi, protozoa, and algae apart from one another using structural and/or functional characteristics. You can find answers in