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1 The Evolution of Microorganisms and

This chapter introduces the field of microbiology and discusses the importance of microorganisms not only as causative agents of disease, but also as important contributors to food production, antibiotic manufacture, vaccine development, and environmental management. It presents a brief history of the science of microbiology and an overview of the microbial world. The origin of life and microbial evolution is put in the context of microbial phylogenies.

After reading this chapter you should be able to: define the science of microbiology and describe some of the general methods used in the study of microorganisms discuss the historical concept of spontaneous generation and the experiments that were performed to disprove this erroneous idea discuss how Kochs postulates are used to establish the causal link between a suspected microorganism and a disease describe some of the various activities of microorganisms that are beneficial to humans describe prokaryotic and eukaryotic morphology and the distribution of microorganisms among the three domains in which living organisms are categorized discuss the origin of life, the RNA world, and the evolution of microorganisms

CHAPTER OUTLINE I.MicrobiologyIntroduction A. Microbes are found everywhere and are indispensable for cycling of essential
elements on earth

B. Most microbes are beneficial to society by producing foods, oxygen, and

commercial products, and by enhancing human health; some microbes cause disease II.Members of the Microbial World A. Microbiology is the study of organisms too small to be clearly seen by the unaided eye (i.e., microorganisms); these include viruses, bacteria, archaea, protozoa, algae, and fungi

Some microbes (e.g., algae and fungi) are large enough to be visible, but are still included in the field of microbiology; while these may be multicellular organisms, differentiated tissues are absent C. Prokaryotes have a relatively simple morphology and lack a true membranedelimited nucleus D. Eukaryotes are morphologically complex and have a true, membraneenclosed nucleus E. The work of Carl Woese and his collaborators suggests that organisms fall into one of three domains based on nucleotide sequence similarities among small subunit ribosomal RNAs (SSU rRNAs) 1. Eukaryacontains all eukaryotic organisms; have a complex membrane-delimited organelle structure 2. Bacteriadiverse and widespread prokaryotes; cell walls contain peptidoglycan 3. Archaeaprokaryotes with cell walls that lack peptidoglycan; have unique membrane lipids F. Viruses, viroids, virusoids, and prions are not composed of cells and not part of the domain classification scheme III. Microbial Evolution A. Evidence for the origin of life 1. Earth is about 4.6 billion years old; what appear to be the fossilized remains of 3.5-billion-year-old prokaryotic cells have been found in stromatolites and sedimentary rocks 2. Extant organisms have been suggested to contain structures and molecules that are relics of ancient life forms B. RNA world 1. It is speculated in the RNA world theory that the first self-replicating molecules were RNAs that stored information and had catalytic activity (ribozymes); eventually DNA became the molecule for information storage and proteins became the molecules with catalytic activity 2. The earliest prokaryotes were probably anaerobic and lithotrophs 3. Cyanobacteria probably developed oxygenic photosynthesis 2.5 billion years ago forming layered rocks called stromatolites (stratified rocks that are formed by incorporation of mineral sediments into microbial mats) C. Evolution of the three domains of life 1. The universal phylogenetic tree is based on comparisons of small subunit rRNA molecules such that evolutionary distances are shown 2. The last universal common ancestor (LUCA) sits at the root of the tree on the bacterial branch; the nature of this organism is unclear 3. The endosymbiotic origin of mitochondria, chloroplasts, and hydrogenosomes a. Endosymbiotic theory states that these organelles arose from prokaryotes that lived within eukaryotic cells, eventually losing parts of their genome to the host cell and thereby losing the ability to survive independently; organelles have both circular chromosomes related to bacterial genomes and independent transcription and translation systems b. The hydrogen hypothesis states that the progenitor of mitochondria was a bacterium that produced hydrogen through fermentation that was required by the host; the hydrogenosome may be another relic of this early symbiont 4. Cellular life forms developed through the same evolutionary processes seen today including mutation and horizontal gene transfer 2


Since prokaryotic organisms generally do not reproduce sexually, species are defined as groups of strains (pure cultures) sharing stable distinguishing properties; microbiologists use the binomial system for naming species IV. Microbiology and Its Origins A. Microscopy and the discovery of microorganisms 1. Invisible living creatures were thought to exist and were thought to be responsible for disease long before they were observed; the field of microbiology developed as the tools used to study microbes developed 2. Antony van Leeuwenhoek (16321723) constructed microscopes and is credited as the first person to observe and describe microorganisms accurately; Robert Hooke published the first drawings of microorganisms B. Culture-based methods for studying microorganisms 1. Spontaneous generation a. The proponents of the concept of spontaneous generation claimed that living organisms could develop from nonliving or decomposing matter b. Francesco Redi (16261697) challenged this concept by showing that maggots on decaying meat came from fly eggs deposited on the meat, and not from the meat itself c. John Needham (17131781) showed that mutton broth boiled in flasks and then sealed could still develop microorganisms, which supported the theory of spontaneous generation d. Lazzaro Spallanzani (17291799) showed that flasks sealed and then boiled had no growth of microorganisms, and he proposed that air carried germs to the culture medium; he also commented that external air might be needed to support the growth of animals already in the medium; the latter concept was appealing to supporters of spontaneous generation e. Theodore Schwann (18101882) and others carried out experiments testing the need for air if growth was to occur f. Louis Pasteur (18221895) heated the necks of flasks, drawing them out into long curves, sterilized the media, and left the flasks open to the air; no growth was observed because particles carrying organisms did not reach the medium, instead they were trapped in the neck of the flask; if the necks were broken, particles would enter the flasks and the organisms would grow; in this way Pasteur disproved the theory of spontaneous generation g. John Tyndall (18201893) demonstrated that dust carried microbes and that if dust was absent, the broth remained sterileeven if it was directly exposed to air; Tyndall also provided evidence for the existence of heat-resistant forms of bacteria C. Microorganisms and disease 1. Agostino Bassi (17731856) showed that a silkworm disease was caused by a fungus, the first demonstration of microbes causing disease 2. Louis Pasteur showed that the pbrine disease of silkworms was caused by a protozoan parasite; he demonstrated that alcoholic fermentations were performed by yeasts under anaerobic conditions and that different fermentation products were produced by different microorganisms; he developed the process of pasteurization used to preserve wine and milk during storage


Joseph Lister (18721912) developed a system of surgery designed to prevent microorganisms from entering wounds; his patients had fewer postoperative infections, thereby providing indirect evidence that microorganisms were the causal agents of human disease; his published findings transformed the practice of surgery D. Koch's postulates 1. Robert Koch (18431910), using criteria developed by his teacher, Jacob Henle (18091895), established the relationship between Bacillus anthracis and anthrax; his criteria became known as Kochs postulates and are still used to establish the link between a particular microorganism and a particular disease: a. The microorganism must be present in every case of the disease, but absent from healthy individuals b. The suspected microorganism must be isolated and grown in pure culture c. The same disease must result when the isolated microorganism is inoculated into a healthy host d. The same microorganism must be isolated again from the diseased host 2. Kochs work with anthrax was independently confirmed by Pasteur E. Pure culture methods 1. Koch and his associates developed techniques, reagents, and other materials for culturing bacterial pathogens on solid growth media; agar plates enable microbiologists to isolate microbes in pure culture 2. Charles Chamberland (18511908) constructed a bacterial filter that removed bacteria and larger microbes from specimens; this led to the discovery of viruses as disease-causing agents F. Immunology 1. Edward Jenner used a vaccination procedure to protect individuals from smallpox 2. Louis Pasteur developed other vaccines including those for chicken cholera, anthrax, and rabies 3. Emil von Behring (18541917) and Shibasaburo Kitasato (18521931) induced the formation of diphtheria-toxin antitoxins in rabbits; the antitoxins (actually antibodies) were effectively used to treat humans and provided evidence for humoral (antibody) immunity 4. Elie Metchnikoff (18451916) described phagocytic cells in the blood, thus demonstrating cell-mediated immunity G. Microbial ecology 1. Sergei Winogradsky (18561953) worked with soil bacteria and discovered that they could oxidize iron, sulfur, and ammonia to obtain energy; he also studied anaerobic nitrogen fixation and cellulose decomposition 2. Martinus Beijerinck (18511931) isolated aerobic nitrogen-fixing bacteria, a root-nodule bacterium capable of fixing nitrogen, and sulfate-reducing bacteria 3. Beijerinck and Winogradsky pioneered the use of enrichment cultures and selective media to isolate microorganisms that can eat and/or breathe inorganic minerals V.Microbiology Today A. Research in both basic and applied microbiology has an impact on many fields including medicine, agriculture, food science, ecology, genetics, biochemistry, and molecular biology B. Molecular and genomic methods of studying microbes 4





Manipulating DNA in microorganisms is central to studying their relationships and nature 2. The genome (all the genetic information) of an organism can be analyzed using methods leading to determination of the base sequence of genes 3. Genomic analysis defines functions of genes, their regulation, and how they form biological systems Major fields in microbiology 1. Medical microbiology - the study of infectious disease in humans and animals, identifying the causative agents and planning measures for their control 2. Public health microbiology and epidemiology - the study of the mechanisms by which diseases spread and the monitoring of the amount of disease in populations 3. Immunology - study of how the body's immune system protects against infectious disease; includes the study of allergies and autoimmune diseases 4. Microbial ecology - study of the ecological role of microbes in biogeochemical cycles and the interaction of microbes with each other and their habitat 5. Agricultural microbiology - study of the impact of microbes on agriculture, including aspects of nutrient cycles, animal husbandry, and plant pathogens 6. Food and dairy microbiology - study of the use of microbes in food production, food spoilage, and food-borne diseases 7. Industrial microbiology - study of the use of microorganisms in the manufacture of antibiotics, vaccines, chemicals, enzymes, vitamins, and other products More basic research fields of microbiology include microbial physiology, microbial genetics, molecular biology, and bioinformatics


____ 1. Study of organisms too small to be individually observed with the unaided eye ____ 2. Organisms composed of many different cells ____ 3. Microorganisms with cells that do not contain a nucleus ____ 4. A class of acellular microbes that are infectious agents ____ 5. Organisms with cells that contain a nucleus ____ 6. Rocklike structures formed by ancient microbial mats of cyanobacteria ____ 7. Organisms that are present in the biosphere today ____ 8. Molecules of RNA that have enzymatic activity ____ 9. Microbes that use inorganic chemicals as electron sources ____ 10. Organisms that cannot grow in the presence of oxygen ____ 11. The root of the phylogenetic tree that is the progenitor of all current organisms ____ 12. The currently accepted explanation of how the organelles mitochondria, chloroplasts, and hydrogenosomes arose ____ 13. An experimental scheme used to demonstrate the causative agent of an infectious disease ____ 14. A research tool that allows microbial isolates to be grown and separated ____ 15. All of the DNA in a cell a. b. agar plates anaerobes 5

c. d. e. f. g. h. i. j. k. l. m. n. o.

endosymbiotic theory eukaryotes extant organisms genome Koch's postulates last universal common ancestor lithotrophs microbiology multicellular prokaryotes ribozymes stromatolites viruses

From the list below, select the area that best matches the description in each of the numbered statements. ____ 1. Deals with diseases of humans and animals ____ 2. Endeavors to control the spread of communicable diseases ____ 3. Deals with the mechanisms by which the human body protects itself from disease-causing organisms ____ 4. Deals with microorganisms that cause damage to crops or live in herds of domestic animals; also deals with ways of increasing soil fertility ____ 5. Studies the relationship between microorganisms and their habitats ____ 6. Investigates the causes of spoilage of products for human consumption and the use of microorganisms in the production of cheese, yogurt, pickles, beer, etc. ____ 7. Employs microorganisms to make products such as antibiotics, vaccines, steroids, alcohols, vitamins, amino acids, and enzymes ____ 8. Investigates the synthesis of antibiotics and toxins, microbial energy production, the ways in which microorganisms survive harsh environmental conditions, etc. ____ 9. Focuses on the nature of genetic information and how genes regulate the development and function of cells and organisms ____ 10. Involves the insertion of new genes into organisms in order to investigate the genes functions or to produce useful organisms with new properties a. b. c. d. e. f. g. h. i. j. agricultural microbiology food and dairy microbiology genetic engineering immunology industrial microbiology medical microbiology microbial ecology microbial physiology molecular biology public health microbiology


1. The concept that living organisms could develop from nonliving or decomposing matter is referred to as 6








. An Italian physician named ____________ challenged this by showing that maggots developed from fly eggs, not from decaying meat as had previously been thought. However, even after this, many thought that simple microorganisms could develop from nonliving material, even if more complex organisms could not. This was finally disproved by the work of a French scientist named ____________ and an English physicist named ____________, who both demonstrated that organisms only developed in sterile broth exposed to air if dust particles carrying living organisms dropped into the broth. Indirect evidence that microorganisms were agents of human disease came from the work of an English surgeon named ____________, who developed a procedure for antiseptic surgery in which he heat-sterilized his surgical instruments before use and also sprayed the compound phenol, which kills bacteria, over the surgical area. These procedures lowered the incidence of postoperative infections. and discovered that older cultures of the bacterium that caused chicken cholera lost their ability to cause disease, or were said to be ____________. If chickens were injected with these older strains, they remained healthy but developed the ability to resist disease. They called this culture a ____________ in honor of the English physician ______________, who developed the procedure in order to protect against smallpox. Inactivated toxin from the microorganism that causes diphtheria was injected into rabbits by ____________ and ____________, inducing the rabbits to produce a soluble substance in the blood that would neutralize the toxin and protect against disease. This is referred to as ____________ immunity. Taking a different approach, Elie Metchnikoff discovered that some blood cells were capable of ingesting bacteria and thereby destroying them. He called this process ____________, and the cells that can do this, ____________. This is the basis for cell-mediated immunity. The theory that yeast cells were responsible for converting sugar to alcohol was first proposed by ____________ and others. However, it was ____________ who did the definitive work that clearly demonstrated this to be true. One of his most important discoveries was that some organisms carried out these processes ____________ (in the presence of oxygen) while others carried them out ____________ (in the absence of oxygen). Two of the most important contributors in the field of microbial ecology were ____________, who discovered that soil bacteria could oxidize iron, sulfur, and ammonia to obtain energy, and ____________, who isolated a root-nodule bacterium capable of nitrogen fixation. These individuals also pioneered the use of ____________ __________ techniques and __________ media. Scientists begin their attempts to understand natural phenomena by gathering observations on a topic and then formulating an , which is subsequently tested experimentally. If this initial educated guess about the phenomenon of interest survives the testing, it may become a , which is a set of propositions and concepts that provides a reliable, systematic, and rigorous account of an aspect of nature. The two prokaryotic domains are and , while plants and animals are in the domain .

For each of the questions below select the one best answer. 1. Which of the following is (are) used to define the field of microbiology? a. the size of the organism studied 7 b. c. the techniques employed in the study of organisms regardless of their size Both (a) and (b) are correct.


Neither (a) nor (b) is correct.

2. Which of the following developed a set of criteria that could be used to establish a causative link between a particular microorganism and a particular disease? a. van Leeuwenhoek b. Fracastoro c. Pasteur d. Koch

3. Which of the following was the first to observe and accurately describe microorganisms? a. van Leeuwenhoek b. Fracastoro c. Pasteur d. Koch 4. Which of the following provided strong evidence against the concept of spontaneous generation? a. van Leeuwenhoek b. Fracastoro c. Pasteur d. Koch


Which of the following provided evidence that a microorganism could be responsible for a particular disease? a. Bassi b. Berkeley c. Koch d. All of the above are correct. Which of the following has been suggested as the central molecule in the precellular stage of life's origins? a. DNA b. Proteins c. RNA d. Lipids


____ 1. ____ 2. ____ 3. ____ 4. ____ 5. Although Robert Koch used and published the criteria for establishing a causative link between a particular microorganism and a particular disease, the criteria were actually first developed by his former teacher, Jacob Henle. The major difference between prokaryotic cells and eukaryotic cells is that eukaryotic cells have a membrane-bound nucleus but prokaryotic cells do not. Agar is used instead of gelatin to solidify microbial media because agar is not digested by many bacteria while gelatin is. The first disease to be identified as being caused by a virus was anthrax. The discovery of viruses and their role in disease was made possible when Charles Chamberland constructed a porcelain filter that would retain bacteria. Using these filters, others found that some disease-causing organisms were not retained by the filter; these were referred to as viruses. Louis Pasteur was the first to document the use of a vaccination procedure to prevent disease. Microorganisms can be used in bioremediation to reduce pollution effects. Genetically engineered microorganisms are used to produce a variety of products including hormones, antibiotics, and vaccines. Recent advances in classification led to the proposal that organisms should be divided into three domains: Archaea, Bacteria, and Eukarya.

____ 6. ____ 7. ____ 8. ____ 9.

1. Discuss the spontaneous generation theory. Present the evidence that was used to support it and present the evidence that was used to discredit it. How was this theory finally discredited?

2. Describe in detail at least two ways in which microorganisms have a direct and substantial impact on your life (other than as causative agents of disease). Include a discussion of the role(s) of the microorganisms in these processes.

3. In the 1980s when AIDS was first recognized, scientists were faced with the task of identifying the causative agent. Suppose you were one of those scientists and that you observed a virus in the tissues of AIDS patients. Which steps of Kochs postulate could you use to support your belief that the virus was responsible for the disease? Which steps couldnt you use? Explain your answers.

Terms and Definitions 1. j, 2. k, 3. l, 4. o, 5. d, 6. n, 7. e, 8. m, 9. i, 10. b, 11. h, 12. c, 13. g, 14. a, 15. f Areas of Microbiology 1. f, 2. j, 3. d, 4. a, 5. g, 6. b, 7. e, 8. h, 9. i, 10. c Fill in the Blank 1. spontaneous generation; Francesco Redi; Louis Pasteur; John Tyndall 2. Joseph Lister 3. Pasteur; Roux; attenuated; vaccine; Jenner 4. Emil von Behring; Shibasaburo Kitasato; humoral; phagocytosis; phagocytes 5. Theodore Schwann; Louis Pasteur; aerobically; anaerobically 6. Sergius Winogradsky; Martinus Beijerinck; enrichment culture; selective 7. hypothesis; theory 8. Bacteria; Archaea; Eukarya Multiple Choice 1. c, 2. d, 3. a, 4. c, 5. d, 6. c


True/False 1. T, 2. T, 3. T, 4. F, 5. T, 6. F, 7. T, 8. T, 9. T