1

Dans les champs de l’observation, le hasard ne favorise que les esprits préparés. (In the field of observation, chance favors only prepared minds.)

—Louis Pasteur

Louis Pasteur, one of the greatest scientists of the nineteenth century, maintained that “Science knows no country, because knowledge be-longs to humanity, and is a torch which illuminates the world.”

Chapter Glossary

The History and Scope of Microbiology

The importance of microorganisms cannot be overemphasized. In terms of sheer number and mass—microbes contain an estimated 50% of the biological carbon and 90% of the biological nitrogen on Earth—they greatly exceed every other group of organisms on the planet. Furthermore, they are found everywhere: from geothermal vents in the ocean depths to the coldest Arctic ice. They are major contributors to the functioning of the biosphere, being indispens-able for the cycling of the elements essential for life. They also are

a source of nutrients at the base of all ecological food webs. Most important, certain microorganisms carry out photosynthesis, rivaling plants in their role of capturing carbon dioxide and releasing oxygen into the atmosphere. Those microbes that inhabit humans are also important, helping the body digest food and producing vitamins B and K. In addition, society in general benefi ts from microorganisms. Indeed, modern biotechnology rests upon a microbiological founda-tion, as microbes are necessary for the production of bread, cheese,

Archaea The domain of life that contains procaryotic cells with cell walls that lack peptidoglycan; they have unique lipids in their membranes and archaeal rRNA (among many differences).

Bacteria The domain of life that contains procaryotic cells with cell walls that contain the structural molecule peptidoglycan; they have bacterial rRNA.

Eucarya The domain of life that features organisms made of cells that have a membrane-delimited nucleus and differ in many other ways from procaryotic cells; includes protists, fungi, plants, and animals.

fungi A diverse group of microorganisms that range from unicellular forms (yeasts) to multicellular molds and mushrooms.

Koch’s postulates A set of rules for proving that a specifi c microorganism causes a particular disease.

microbiology The study of organisms that are usually too small to be seen with the naked eye; special techniques are required to isolate and grow them.

microorganism An organism that is too small to be seen clearly with the naked eye and lacks highly differentiated cells and distinct tissues.

prions Infectious agents that cause spongiform encephalopa-thies such as scrapie in sheep; they are composed only of protein.

procaryotic cells Cells that lack a true, membrane-enclosed nucleus; Bacteria and Archaea are procaryotic and have their genetic material located in a nucleoid.

protists Mostly unicellular eucaryotic organisms that lack cel-lular differentiation into tissues; cell differentiation is limited to cells involved in sexual reproduction, alternate vegetative mor-phology, or resting states such as cysts; includes organisms often referred to as algae and protozoa.

spontaneous generation An early belief, now discredited, that living organisms could develop from nonliving matter.

viroids Infectious agents composed only of single-stranded, circular RNA; they cause numerous plant diseases.

viruses Infectious agents having a simple acellular organiza-tion with a protein coat and a nucleic acid genome, lacking independent metabolism, and reproducing only within living host cells.

virusoids Infectious agents composed only of single-stranded RNA; they are unable to replicate without the aid of specifi c viruses that coinfect the host cell.

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2 Chapter 1 The History and Scope of Microbiology

beer, antibiotics, vaccines, vitamins, enzymes, and many other prod-ucts. Their ability to produce biofuels such as ethanol is also being intensively explored. These alternative fuels are both renewable and can help decrease pollution associated with burning fossil fuels. Although most microorganisms play benefi cial or benign roles, some harm humans and have disrupted society over the millen-nia. Microbial diseases undoubtedly played a major role in historical events such as the decline of the Roman Empire and the conquest of the New World. In 1347, plague (Black Death), an arthropod-borne disease, struck Europe with brutal force, killing one-third of the population (about 25 million people) within four years. Over the next 80 years, the disease struck repeatedly, eventually wiping out 75% of the European population. The plague’s effect was so great that some historians believe it changed European culture and prepared the way for the Renaissance. Today the struggle by microbiologists and others against killers such as AIDS and malaria continues. In this chapter, we introduce the microbial world to provide a gen-eral idea of the organisms and agents that microbiologists study. We next discuss the scope and relevance of modern microbiology. Finally, we describe the historical development of the science of microbiology and its relationship to medicine and other areas of biology.

1.1 MEMBERS OF THE MICROBIAL WORLD

Microbiology often has been defi ned as the study of organisms and agents too small to be seen clearly by the unaided eye—that is, the study of microorganisms . Because objects less than about 1 millimeter in diameter cannot be seen clearly and must be exam-ined with a microscope, microbiology is concerned primarily with organisms and agents this small and smaller. However, some microorganisms, particularly some eucaryotic microbes, are visible without microscopes. For example, bread molds and fi lamentous algae are studied by microbiologists yet are visible to the naked eye, as are the two bacteria Thiomargarita and Epulopiscium. >> Microbial Diversity & Ecology 3.1: Monstrous Microbes The diffi culty in setting the boundaries of microbiology has led to the suggestion of other criteria for defi ning the fi eld. For instance, an important characteristic of microorganisms, even those that are large and multicellular, is that they are relatively simple in their construction, lacking highly differentiated cells and distinct tis-sues. Another suggestion, made by Roger Stanier, is that the fi eld also be defi ned in terms of its techniques. Microbiologists usually fi rst isolate a specifi c microorganism from a population and then culture it. Thus microbiology employs techniques—such as sterilization and the use of culture media—that are necessary for successful isolation and growth of microorganisms. Microorganisms are diverse, and their classifi cation has always been a challenge for microbial taxonomists. Their early descrip-tions as either plants or animals were too simple. For instance, some microbes are motile like animals but also have cell walls and

are photosynthetic like plants. Such microbes cannot be placed easily into one kingdom or another. Another important factor in classifying microorganisms is that some are composed of procary-otic cells and others of eucaryotic cells. Procaryotic cells (Greek pro, before, and karyon, nut or kernel; organisms with a primordial nucleus) have a much simpler morphology than eucaryotic cells and lack a true membrane-delimited nucleus. In contrast, eucary-otic cells (Greek eu, true, and karyon, nut or kernel) have a membrane-enclosed nucleus; they are more complex morphologi-cally and are usually larger than procaryotes. These observations eventually led to the development of a classifi cation scheme that divided organisms into fi ve kingdoms: the Monera, Protista, Fungi, Animalia, and Plantae. Microorganisms (except for viruses and other acellular infectious agents, which have their own classifi ca-tion system) were placed in the fi rst three kingdoms. In the last few decades, great progress has been made in three areas that profoundly affect microbial classifi cation. First, much has been learned about the detailed structure of microbial cells from the use of electron microscopy. Second, microbiologists have deter-mined the biochemical and physiological characteristics of many different microorganisms. Third, the sequences of nucleic acids and proteins from a wide variety of organisms have been compared. The comparison of ribosomal RNA (rRNA), begun by Carl Woese in the 1970s, was instrumental in demonstrating that there are two very different groups of procaryotic organisms: Bacteria and Archaea, which had been classifi ed together as Monera in the fi ve-kingdom system. Later studies based on rRNA comparisons showed that Protista is not a cohesive taxonomic unit and that it should be divided into three or more kingdoms. These studies and others have led many taxonomists to conclude that the fi ve-kingdom system is too simple. A number of alternatives have been suggested, but cur-rently most microbiologists believe that organisms should be divided among three domains: Bacteria (the true bacteria or eubacteria), Archaea, 1 and Eucarya (all eucaryotic organisms) ( fi gure 1.1 ). We use this system throughout the text, and it is dis-cussed in detail in chapter 17. However, a brief description of the three domains and of the microorganisms placed in them follows.

Bacteria 2 are procaryotes that are usually single-celled organ-isms. Most have cell walls that contain the structural molecule peptidoglycan. They are abundant in soil, water, and air, and are major inhabitants of our skin, mouth, and intestines. Some bacte-ria live in environments that have extreme temperatures, pH, or salinity. Although some bacteria cause disease, many more play benefi cial roles such as cycling elements in the biosphere, break-ing down dead plant and animal material, and producing vitamins. Cyanobacteria (once called blue-green algae) produce signifi cant amounts of oxygen through the process of photosynthesis.

Archaea are procaryotes that are distinguished from Bacteria by many features, most notably their unique ribosomal RNA sequences. They lack peptidoglycan in their cell walls and have unique membrane lipids. Some have unusual metabolic

1 Although this is discussed further in chapter 17, it should be noted here that several names have been used for the Archaea. The two most important are archaeobacteria and archaebacteria. In this text, we use only the name Archaea.

2 In this text, the term bacteria (s., bacterium) is used to refer to procaryotes that belong to domain Bacteria, and the term archaea (s., archaeon) is used to refer to procaryotes that belong to domain Archaea. In some publications, the term bacteria is used to refer to all procaryotes. That is not the case in this text.

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characteristics, such as the methanogens, which generate meth-ane gas. Many archaea are found in extreme environments, including those with high temperatures (thermophiles) and high concentrations of salt (extreme halophiles). Pathogenic archaea have not yet been identifi ed. Domain Eucarya includes microorganisms classifi ed as pro-tists or fungi. Animals and plants are also placed in this domain. Protists are generally unicellular but larger than procaryotes. Photosynthetic protists, together with the cyanobacteria, produce about 75% of the planet’s oxygen. These phytoplankton are the foundation of aquatic food chains. Protozoa are unicellular, animal-like protists that are usually motile. Many free-living protozoa function as the principal hunters and grazers of the microbial world. They obtain nutrients by ingesting organic matter and other microbes. They can be found in many different environments, and some are normal inhabitants of the intestinal tracts of animals, where they aid in digestion of complex materials such as cellulose. A few cause disease in humans and other animals. Slime molds are protists that are like protozoa in one stage of their life cycle but like fungi in another. In the protozoan phase, they hunt for and engulf food particles, consuming decaying vegetation and other microbes. Water molds are protists that grow on the surface of freshwater and moist soil. They feed on decaying vegetation such as logs and mulch. Some water molds have produced devastating plant infec-

tions, including the Great Potato Famine of 1846–1847 in Ireland. Fungi are a diverse group of microorganisms that range from unicellular forms (yeasts) to molds and mushrooms. Molds and mushrooms are multicellular fungi that form thin, threadlike struc-tures called hyphae. They absorb nutrients from their environment, including the organic molecules that they use as a source of carbon and energy. Because of their metabolic capabilities, many fungi play benefi cial roles, including making bread rise, producing anti-biotics, and decomposing dead organisms. Some fungi associate with plant roots to form mycorrhizae. Mycorrhizal fungi transfer nutrients to the roots, improving the growth of the plants, especially in poor soils. Other fungi cause plant diseases (e.g., rusts, powdery mildews, and smuts) and diseases in humans and other animals. The microbial world also includes numerous acellular infec-tious agents. Viruses are acellular entities that must invade a host cell to replicate. The simplest viruses are composed only of pro-teins and a nucleic acid, and can be extremely small (the smallest is 10,000 times smaller than a typical bacterium). However, their small size belies their power—they cause many animal and plant diseases and have caused epidemics that have shaped human his-tory. The diseases they cause include smallpox, rabies, infl uenza, AIDS, the common cold, and some cancers. Viroids and virusoids are infectious agents composed only of ribonucleic acid (RNA). Viroids cause numerous plant diseases, whereas virusoids cause some important animal diseases such as hepatitis. Finally, prions , infectious agents composed only of protein, are responsible for causing a variety of spongiform encephalopathies such as scrapie and “mad cow disease.”

1. Describe the fi eld of microbiology in terms of the size of its subject material and the nature of its techniques.

2. Describe and contrast procaryotic and eucaryotic cells.

1.2 SCOPE AND RELEVANCE OF MICROBIOLOGY

As the scientist-writer Steven Jay Gould (1941–2002) emphasized, we live in the age of bacteria. They were the fi rst living organisms on our planet, likely created the atmosphere that allowed the evolution of oxygen-consuming life-forms, and now live virtually everywhere life is possible. Furthermore, the biosphere depends on their activities, and they infl uence human society in countless ways. Because microorganisms play such diverse roles, modern microbiology is a large discipline with many different specialties; it has a great impact on fi elds such as medicine, agricultural and food sciences, ecology, genetics, biochemistry, and molecular biology. One indication of the importance of microbiology is the Nobel Prize given for work in physiology or medicine. About one-third of these prizes have been awarded to scientists working on microbiological problems ( see inside front cover ). Microbiology has both basic and applied aspects. The basic aspects are concerned with the biology of microorganisms them-selves. The applied aspects are concerned with practical problems such as disease, water and wastewater treatment, food spoilage

Figure 1.1 Universal Phylogenetic Tree. These evolutionary relationships are based on rRNA sequence comparisons. The human genus (Homo) is highlighted in red.

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1.2 Scope and Relevance of Microbiology 3

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4 Chapter 1 The History and Scope of Microbiology

and food production, and industrial uses of microbes. It is impor-tant to note that the basic and applied aspects of microbiology are intertwined. Basic research is often conducted in applied fi elds, and applications often arise out of basic research. A discussion of some of the major fi elds of microbiology and the occupations within them follows. Although pathogenic microbes are the minority, they garner considerable interest. Thus, one of the most active and important fi elds in microbiology is medical microbiology, which deals with diseases of humans and animals. Medical microbiologists iden-tify the agents causing infectious diseases and plan measures for their control and elimination. Frequently they are involved in tracking down new, unidentifi ed pathogens such as the agent that causes variant Creutzfeldt-Jakob disease (the human version of “mad cow disease”), hantavirus, West Nile virus, and the virus responsible for SARS. These microbiologists also study the ways in which microorganisms cause disease. >> Microbial Diversity & Ecology 24.1: SARS: Evolution of a virus As noted earlier, major epidemics have regularly affected human history. The 1918 infl uenza pandemic is of particular note; it killed more than 20 million people in about one year. Public health microbiology is concerned with the control and spread of such communicable diseases. Public health microbiol-ogists and epidemiologists monitor the amount of disease in populations. Based on their observations, they can detect out-breaks and developing epidemics, and implement appropriate control measures in response. They also conduct surveillance for new diseases as well as bioterrorism events. Those public health microbiologists working for local governments monitor commu-nity food establishments and water supplies in an attempt to keep them safe and free from infectious disease agents. Immunology is concerned with how the immune system pro-tects the body from pathogens and the response of infectious agents. It is one of the fastest growing areas in science. Much of the growth began with the discovery of HIV, which specifi cally targets cells of the immune system. Immunology also deals with health problems such as the nature and treatment of allergies and autoimmune diseases such as rheumatoid arthritis. >> Techniques & Applications 29.1: Monoclonal antibody technology Agricultural microbiology is concerned with the impact of microorganisms on agriculture. Microbes such as nitrogen-fi xing bacteria play critical roles in the nitrogen cycle and affect soil fer-tility. Other microbes live in the digestive tracts of ruminants such as cattle and break down the plant materials these animals ingest. There are also plant and animal pathogens that can have signifi cant economic impacts if not controlled. Agricultural microbiologists work on methods to increase soil fertility and crop yields, study rumen microorganisms in order to increase meat and milk produc-tion, and try to combat plant and animal diseases. Currently many agricultural microbiologists are studying the use of bacterial and viral insect pathogens as substitutes for chemical pesticides. Microbial ecology is concerned with the relationships between microorganisms and the components of their living and nonliving habitats. Microbial ecologists study the global and local contributions of microorganisms to the carbon, nitrogen, and sulfur cycles, including the role of microbes in both the

production and removal of greenhouse gases such as carbon dioxide and methane. The study of pollution effects on microor-ganisms also is important because of the impact these organisms have on the environment. Microbial ecologists are employing microorganisms in bioremediation to reduce pollution. The study of the microbes normally associated with the human body has become a new frontier in microbial ecology. Numerous foods are made using microorganisms. On the other hand, some microbes cause food spoilage or are pathogens spread through food. An excellent example of the latter is Escherichia coli O157:H7, which in 2006 caused a widespread outbreak of dis-ease when it contaminated a major source of spinach in the United States. Scientists working in food and dairy microbiology con-tinue to explore the use of microbes in food production. They also work to prevent microbial spoilage of food and the transmis-sion of food-borne diseases. There is also considerable research on the use of microorganisms themselves as a nutrient source for livestock and humans. >> Microbiology of food (chapter 34) In 1929 Alexander Fleming discovered that the fungus Penicillium produced what he called penicillin, the fi rst antibiotic that could successfully control bacterial infections. Although it took World War II for scientists to learn how to mass-produce it, scientists soon found other microorganisms capable of producing additional antibiotics as well as compounds such as citric acid, vitamin B12, and monosodium glutamate (MSG). Today, indus-trial microbiologists use microorganisms to make products such as antibiotics, vaccines, steroids, alcohols and other solvents, vitamins, amino acids, and enzymes. Industrial microbiologists identify microbes of use to industry. They also utilize techniques to improve production by microbes and devise systems for cul-turing them and isolating the products they make. Microbes are metabolically diverse and can employ a wide variety of energy sources, including organic matter, inorganic molecules (e.g., H 2 and NH 3 ), and sunlight. Microbiologists working in microbial physiology and biochemistry study many aspects of the biology of microorganisms, including their metabolic capabilities. They may also study the synthesis of anti-biotics and toxins, the ways in which microorganisms survive harsh environmental conditions, and the effects of chemical and physical agents on microbial growth and survival. Microbial genetics and molecular biology focus on the nature of genetic information and how it regulates the development and function of cells and organisms. The bacteria E. coli and Bacillus subtilis, the yeast Saccharomyces cerevisiae (baker’s yeast), and bacterial viruses such as T4 and lambda continue to be important model organisms used to understand biological phenomena. Microbial geneticists also play a signifi cant role in applied microbiology because they develop techniques that are useful in agricultural microbiology, industrial microbiology, food and dairy microbiology, and medicine. Because of the practical importance of microbes and their use as model organisms, the future of microbiology is bright. However, it is important to remember that future advances in microbiology will build on the foundations laid by earlier scien-tists. The development of microbiology as a science is described in sections 1.3 to 1.5. Figure 1.2 presents a summary of some of

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