Chapter 1 - The Microbial World and You

4. Most bacteria - have peptidoglycan cell wall - divide by binary fission - may possess flagella

- Most Bacteria • Enclosed in Peptidoglycan (carbohydrate - protein complex) Cell Wall o plant and algal cell walls use cellulose • Reproduce by binary fission - dividing into two equal cells • may have flagella - moving appendages used to swim

Naming and Classifying Microorganisms (pp. 2-6)

Learning Objectives 1-2 Recognize the system of scientific nomenclature that uses two names: a genus and a specific epithet. 1-3 Differentiate the major characteristics of each group of microorganisms. 1-4 List the three domains. Check Your Understanding ✓ Distinguish a genus from a specific epithet. 1-2

5. John Needham claimed that microorganisms could arise spontaneously from heated nutrient broth (1745).

John Needham - claimed - microorganisms arise spontaneously from heated nutrient broth (1745). • The case for spontaneous generation of microorganisms seemed to be strengthened in 1745, when John Needham found that even after he heated chicken broth and corn broth before pouring them into covered flasks, the cooled solutions were soon teeming with microorganisms. • Needham claimed that microbes developed spontaneously from the fluids.

The Golden Age of Microbiology (pp. 7-10) 10. The science of microbiology advanced rapidly between 1857 and 1914.

The Golden Age of Microbiology - 1857 to 1914 • The period from 1857 to 1914 has been appropriately named the Golden Age of Microbiology. • Rapid advances, spearheaded mainly by Pasteur and Robert Koch, led to the establishment of microbiology. • Discoveries included both the agents of many diseases and the role of immunity in preventing and curing disease. • During this productive period, microbiologists studied the chemical activities of microorganisms, improved the techniques for performing microscopy and culturing microorganisms, and developed vaccines and surgical techniques. • Some of the major events that occurred during the Golden Age of Microbiology are listed in Figure 1.4.

14. Joseph Lister introduced the use of a disinfectant to clean surgical wounds in order to control infections in humans (1860s).

Joseph Lister - disinfectant to clean surgical wounds - control infections (1860s). • In the 1860s, Joseph Lister, an English surgeon, applied the germ theory to medical procedures. • Lister was aware that in the 1840s, the Hungarian physician Ignaz Semmelweis had demonstrated that physicians, who at the time did not disinfect their hands, routinely transmitted infections (puerperal, or childbirth, fever) from one obstetrical patient to another. • Lister had also heard of Pasteur's work connecting microbes to animal diseases. • Disinfectants were not used at the time, but Lister knew that phenol (carbolic acid) kills bacteria, so he began treating surgical wounds with a phenol solution. • The practice so reduced the incidence of infections and deaths that other surgeons quickly adopted it. • His findings proved that microorganisms cause surgical wound infections.

22. Alexander Fleming observed that the Penicillium fungus inhibited the growth of a bacterial culture. He named the active ingredient penicillin (1928).

A Fortunate Accident—Antibiotics • The first antibiotic was discovered by accident. o Alexander Fleming, a Scottish physician and bacteriologist, almost tossed out some culture plates that had been contaminated by mold. o Fortunately, he noticed the curious pattern of growth on the plates—a clear area where bacterial growth had been inhibited encircled the mold (Figure 1.5). o Fleming was looking at a mold that inhibited growth of a bacterium. o The mold became known as Penicillium chrysogenum (pen9i-SIL-lē-um krĪ-SO-jen-um), and the mold's active inhibitor was called penicillin. o Thus, penicillin is an antibiotic produced by a fungus. o The enormous usefulness of penicillin was not apparent until the 1940s, when it was finally tested clinically and mass produced. • Since these early discoveries, thousands of other antibiotics have been discovered. o Unfortunately, antibiotics and other chemotherapeutic drugs are not without problems. o Many antimicrobial chemicals kill pathogenic microbes but also damage the infected host. o For reasons we will discuss later, toxicity to humans is a particular problem in the development of drugs for treating viral diseases. o Viral growth depends on life processes of normal host cells. o Thus, there are very few successful antiviral drugs, because a drug that would interfere with viral reproduction would also likely affect uninfected cells of the body.

17. About 1880, Pasteur discovered that avirulent bacteria could be used as a vaccine for fowl cholera.

About 1880, Pasteur discovered that avirulent bacteria could be used as a vaccine for fowl cholera. • Years after Jenner's experiment, Pasteur discovered why vaccinations work. o He found that the bacterium that causes fowl cholera lost its ability to cause disease (lost its virulence, or became avirulent) after it was grown in the laboratory for long periods. o However, it—and other microorganisms with decreased virulence—was able to induce immunity against subsequent infections by its virulent counterparts. o The discovery of this phenomenon provided a clue to Jenner's successful experiment with cowpox. o Both cowpox and smallpox are caused by viruses. o Even though cowpox virus is not a laboratory-produced derivative of smallpox virus, it is so closely related to the smallpox virus that it can induce immunity to both viruses. o Pasteur used the term vaccine for cultures of avirulent microorganisms used for preventive inoculation. o (The Latin word vacca means cow—thus, the term vaccine honored Jenner's earlier cowpox inoculation work.) • Jenner's experiment was actually not the first time a living viral agent—in this case, the cowpox virus—was used to produce immunity. • Starting in the 1500s, physicians in China had immunized patients from smallpox by removing scales from drying pustules of a person suffering from a mild case of smallpox, grinding the scales to a fine powder, and inserting the powder into the nose of the person to be protected.

12. Algae - unicellular or multicellular - eukaryotes - photosynthesize

Algae (singular: alga) • photosynthetic eukaryotes with a wide variety of shapes • both sexual and asexual reproductive forms • The algae of interest to microbiologists are usually unicellular • many algae - cell walls (cellulose) • abundant in freshwater and saltwater, in soil, and in association with plants

13. Algae Nutrition - - produce oxygen and carbohydrates used by other organisms.

Algae Nutrition. As photosynthesizers, algae need light, water, and carbon dioxide for food production and growth, • do not generally require organic compounds from the environment • produce oxygen and carbohydrates that are then utilized by other organisms, including animals • play an important role in the balance of nature.

2. Anton van Leeuwenhoek, using a simple microscope, was the first to observe microorganisms (1673).

Anton van Leeuwenhoek - first to observe microorganisms with a simple microscope. • Though Hooke's microscope was capable of showing large cells, it lacked the resolution that would have allowed him to see microbes clearly. • Dutch merchant and amateur scientist Anton van Leeuwenhoek was probably the first to observe live microorganisms through the magnifying lenses of the more than 400 microscopes he constructed. • Between 1673 and 1723, he wrote about the "animalcules" he saw through his simple, single-lens microscopes. • Van Leeuwenhoek made detailed drawings of organisms he found in rainwater, feces, and material scraped from teeth. • These drawings have since been identified as representations of bacteria and protozoa (Figure 1.2).

6. Archaea - prokaryotic cells - lack peptidoglycan in their cell walls

Archaea • prokaryotic cells • if they have cell walls, the walls lack peptidoglycan • not known to cause disease in humans

7. Archaea include - methanogens - extreme halophiles - extreme thermophiles

Archaea - Extremophiles. Often found in extreme environments - • methanogens - produce methane as a waste product from respiration • extreme halophiles - live in extremely salty environments (Great Salt Lake, Dead Sea) • extreme thermophiles - live in hot sulfurous water (hot springs @Yellowstone National Park)

17. Laboratory Identification of helminths - microscopic stages in the life cycle of helminths - identified by traditional microbiological procedures

Laboratory Identification of helminths. • During some stages of their life cycle, helminths are microscopic in size. • Laboratory identification of these organisms includes many of the same techniques used for identifying microbes.

7. Rudolf Virchow introduced the concept of biogenesis: living cells can arise only from preexisting cells (1858).

The Theory of Biogenesis - Rudolf Virchow • In 1858 Rudolf Virchow challenged the case for spontaneous generation with the concept of biogenesis, hypothesizing that living cells arise only from preexisting living cells. • Because he could offer no scientific proof, arguments about spontaneous generation continued until 1861, when the issue was finally resolved by the French scientist Louis Pasteur.

3. Bacteria - unicellular organisms - prokaryotic - no nucleus

Bacteria (singular: bacterium) • relatively simple, single-celled o prokaryotes - genetic material is not enclosed in a special nuclear membrane o Prokaryotes include both bacteria and archaea • Most common shapes - o Bacillus (rodlike) o coccus (spherical or ovoid) o spiral (corkscrew or curved) • Less common shapes - o starshaped or square • may form pairs, chains, clusters, or other groupings; such formations are usually characteristic of a particular genus or species of bacteria

5. Bacterial Nutrition - wide range of chemical substances

Bacterial Nutrition. • most bacteria use organic chemicals derived from either dead or living organisms • Some can manufacture their own food by photosynthesis • Some can derive nutrition from inorganic substances.

Classification of Microorganisms (pp. 5-6) Check Your Understanding ✓ What are the three domains? 1-4 18. All organisms are classified into Bacteria, Archaea, and Eukarya. Eukarya include protists, fungi, plants, and animals.

Before microbes were known • all organisms were grouped into either the animal kingdom or the plant kingdom. When microscopic organisms were discovered late in the 17th century, • a new system of classification was needed. • biologists couldn't agree on the criteria for classifying these new organisms until the late 1970s. Carl Woese (1978) - devised a system of classification • based on the cellular organization of organisms. • all organisms - in three domains: 1. Bacteria (cell walls contain a protein-carbohydrate complex called peptidoglycan) 2. Archaea (cell walls, if present, lack peptidoglycan) 3. Eukarya, which includes the following: Protists (slime molds, protozoa, and algae) Fungi (unicellular yeasts, multicellular molds, and mushrooms) Plants (mosses, ferns, conifers, and flowering plants) Animals (sponges, worms, insects, and vertebrates)

3. Bacterial communities that form slimy layers on surfaces are called biofilms.

Biofilms • In nature, microorganisms may exist as single cells that float or swim independently in a liquid, or they may attach to each other and/or some usually solid surface. • This latter mode of behavior is called a biofilm, a complex aggregation of microbes. o The slime covering a rock in a lake is a biofilm. o Use your tongue to feel the biofilm on your teeth. • Biofilms can be beneficial. o They protect your mucous membranes from harmful microbes, and biofilms in lakes are an important food for aquatic animals. • Biofilms can also be harmful. o They can clog water pipes, and on medical implants such as joint prostheses and catheters (Figure 1.9), they can cause such infections as endocarditis (inflammation of the heart). o Bacteria in biofilms are often resistant to antibiotics because the biofilm offers a protective barrier. • See the box in Chapter 3 on page 54. Biofilms will be discussed in Chapter 6.

3. Bioremediation processes use bacteria to clean up toxic wastes.

Bioremediation: Using Microbes to Clean Up Pollutants • In 1988, scientists began using microbes to clean up pollutants and toxic wastes produced by various industrial processes. • For example, some bacteria can actually use pollutants as energy sources; others produce enzymes that break down toxins into less harmful substances. • By using bacteria in these ways—a process known as bioremediation—toxins can be removed from underground wells, chemical spills, toxic waste sites, and oil spills, such as the massive oil spill from a British Petroleum offshore drilling rig in the Gulf of Mexico in 2010 (see also the Applications of Microbiology box in Chapter 2, page 31). • In addition, bacterial enzymes are used in drain cleaners to remove clogs without adding harmful chemicals to the environment. • In some cases, microorganisms indigenous to the environment are used; in others, genetically modified microbes are used. • Among the most commonly used microbes are certain species of bacteria of the genera Pseudomonas and Bacillus. • Bacillus enzymes are also used in household detergents to remove spots from clothing.

The Debate over Spontaneous Generation (pp. 6-7) 3. Until the mid-1880s, many people believed in spontaneous generation, the idea that living organisms could arise from nonliving matter.

Debate over Spontaneous Generation. • After van Leeuwenhoek discovered the previously "invisible" world of microorganisms, the scientific community became interested in the origins of these tiny living things. • Until the second half of the nineteenth century, many scientists and philosophers believed that some forms of life could arise spontaneously from nonliving matter; they called this hypothetical process spontaneous generation. • Not much more than 100 years ago, people commonly believed that toads, snakes, and mice could be born of moist soil; that flies could emerge from manure; and that maggots (which we now know are the larvae of flies) could arise from decaying corpses.

5. An emerging infectious disease (EID) is a new or changing disease showing an increase in incidence in the recent past or a potential to increase in the near future.

Emerging Infectious Diseases • These recent outbreaks point to the fact that infectious diseases are not disappearing, but rather seem to be reemerging and increasing. In addition, a number of new diseases—emerging infectious diseases (EIDs)—have cropped up in recent years. These are diseases that are new or changing and are increasing or have the potential to increase in incidence in the near future. Some of the factors that have contributed to the development of EIDs are evolutionary changes in existing organisms (e.g., Vibrio cholerae; VIBrē- ō KOL-er-ī); the spread of known diseases to new geographic regions or populations by modern transportation (e.g., West Nile virus); and increased human exposure to new, unusual infectious agents in areas that are undergoing ecologic changes such as deforestation and construction (e.g., Venezuelan hemorrhagic virus). EIDs also develop as a result of antimicrobial resistance (e.g., vancomycin-resistant S. aureus). An increasing number of incidents in recent years highlights the extent of the problem. • Between April 2012 and June 2014, there were 339 confirmed cases and 100 deaths in humans caused by a new virus called Middle East respiratory syndrome coronavirus (MERS-CoV). The virus belongs to the same family that causes illnesses from the common cold to severe acute respiratory syndrome (SARS), to be described shortly. Because all reported cases are linked to the Middle East, this latest emerging infectious disease is called Middle East respiratory syndrome (MERS). • Severe acute respiratory syndrome (SARS) is an emerging infectious disease that first appeared in China in 2002. It is a viral infection caused by the SARS-associated coronavirus (SARS-CoV). • H1N1 influenza (flu), also known as swine flu, is a type of influenza caused by a new virus called influenza H1N1. H1N1 was first detected in the United States in 2009, and that same year the World Health Organization declared H1N1 flu to be a pandemic disease (a disease that affects large numbers of individuals in a short period of time and occurs worldwide). • Avian influenza A (H5N1), or bird flu, caught the attention of the public in 2003, when it killed millions of poultry and 24 people in southeast Asia. Avian influenza viruses occur in birds worldwide. In 2013, a different avian influenza, H7N9, sickened 131 people in China. • Influenza A viruses are found in many different animals, including ducks, chickens, pigs, whales, horses, and seals. Normally, each subtype of influenza A virus is specific to certain species. However, influenza A viruses normally seen in one species sometimes can cross over and cause illness in another species, and all subtypes of influenza A virus can infect pigs. Although it is unusual for people to get influenza infections directly from animals, sporadic human infections and outbreaks caused by certain avian influenza A viruses and pig influenza viruses have been reported. As of 2008, avian influenza had sickened 242 people, and about half of them died. Fortunately, the virus has not yet evolved to be transmitted successfully among humans. • Human infections with avian influenza viruses detected since 1997 have not resulted in sustained human-to-human transmission. However, because influenza viruses have the potential to change and gain the ability to spread easily between people, monitoring for human infection and person-to-person transmission is important (see the box in Chapter 13 on page 363). • Antibiotics are critical in treating bacterial infections. However, years of overuse and misuse of these drugs have created environments in which antibiotic-resistant bacteria thrive. Random mutations in bacterial genes can make a bacterium resistant to an antibiotic. In the presence of that antibiotic, this bacterium has an advantage over other, susceptible bacteria and is able to proliferate. Antibiotic-resistant bacteria have become a global health crisis. • Staphylococcus aureus causes a wide range of human infections from pimples and boils to pneumonia, food poisoning, and surgical wound infections, and it is a significant cause of hospital-associated infections. After penicillin's initial success in treating S. aureus infection, penicillin-resistant S. aureus became a major threat in hospitals in the 1950s, requiring the use of methicillin. In the 1980s, methicillin-resistant S. aureus, called MRSA, emerged and became endemic in many hospitals, leading to increasing use of vancomycin. In the late 1990s, S. aureus infections that were less sensitive to vancomycin (vancomycin-intermediate S. aureus, or VISA) were reported. In 2002, the first infection caused by vancomycin-resistant S. aureus (VRSA) in a patient in the United States was reported. • In 2010, the World Health Organization (WHO) reported that in some parts of the world (such as northwestern Russia) about 28% of all individuals with tuberculosis (TB) had the multidrug-resistant form of the disease (MDR-TB). Multidrugresistant TB is caused by bacteria that are resistant to at least the antibiotics isoniazid and rifampicin, the most effective drugs against tuberculosis. • The antibacterial substances added to various household cleaning products are similar to antibiotics in many ways. When used correctly, they inhibit bacterial growth. However, wiping every household surface with these antibacterial agents creates an environment in which the resistant bacteria survive. Unfortunately, when you really need to disinfect your homes and hands—for example, when a family member comes home from a hospital and is still vulnerable to infection—you may encounter mainly resistant bacteria. • Routine housecleaning and handwashing are necessary, but standard soaps and detergents (without added antibacterials) are fine for these tasks. In addition, quickly evaporating chemicals, such as chlorine bleach, alcohol, ammonia, and hydrogen peroxide, remove potentially pathogenic bacteria but do not leave residues that encourage the growth of resistant bacteria. • West Nile encephalitis (WNE) is inflammation of the brain caused by West Nile virus (see the Clinical Focus box on page 215). WNE was first diagnosed in the West Nile region of Uganda in 1937. In 1999 the virus made its first North American appearance in humans in New York City. In 2007, West Nile virus infected over 3600 people in 43 states. West Nile virus is now established in nonmigratory birds in 48 states. The virus, which is carried by birds, is transmitted between birds—and to horses and humans—by mosquitoes. West Nile virus may have arrived in the United States in an infected traveler or in migratory birds. • In 1996, countries worldwide were refusing to import beef from the United Kingdom, where hundreds of thousands of cattle born after 1988 had to be killed because of an epidemic of bovine spongiform encephalopathy (en-sef-a-LOP-a-thē), also called BSE or mad cow disease. BSE first came to the attention of microbiologists in 1986 as one of a handful of diseases caused by an infectious protein called a prion. Studies suggest that the source of disease was cattle feed prepared from sheep infected with their own version of the disease. Cattle are herbivores (plant eaters), but adding protein to their feed improves their growth and health. Creutzfeldt-Jakob disease (KROITS-felt YA-kob), or CJD, is a human disease also caused by a prion. The incidence of CJD in the United Kingdom is similar to the incidence in other countries. However, by 2005 the United Kingdom reported 154 human cases of CJD caused by a new variant related to the bovine disease (see Chapter 22). • Escherichia coli is a normal inhabitant of the large intestine of vertebrates, including humans, and its presence is beneficial because it helps produce certain vitamins and breaks down otherwise undigestible foodstuffs (see Chapter 25). However, a strain called E. coli O157:H7 causes bloody diarrhea when it grows in the intestines. This strain was first recognized in 1982 and since then has emerged as a public health problem. It is now one of the leading causes of diarrhea worldwide. In 1996, some 9000 people in Japan became ill, and 7 died, as a result of infection by E. coli O157:H7. The recent outbreaks of E. coli O157:H7 in the United States, associated with contamination of undercooked meat and unpasteurized beverages, have led public health officials to call for the development of new methods of testing for bacteria in food. • In 2004, emergence of a new epidemic strain of Clostridium difficile (klos-TRID-ē-um DIF-fi-sē-il) was reported. The epidemic strain produces more toxins than others and is more resistant to antibiotics. In the United States, C. difficile infections kill nearly 14,000 people a year. Nearly all of the C. difficile infections occur in health care settings, where the infection is frequently transmitted between patients via health care personnel whose hands are contaminated after contact with infected patients or their surrounding environment. • In 1995, a hospital laboratory technician in Democratic Republic of Congo (DROC) who had fever and bloody diarrhea underwent surgery for a suspected perforated bowel. Afterward he started hemorrhaging, and his blood began clotting in his blood vessels. A few days later, health care workers in the hospital where he was staying developed similar symptoms. One of them was transferred to a hospital in a different city; personnel in the second hospital who cared for this patient also developed symptoms. By the time the epidemic was over, 315 people had contracted Ebola hemorrhagic fever (hem-or-RAJ-ik), or EHF, and over 75% of them died. The epidemic was controlled when microbiologists instituted training on the use of protective equipment and educational measures in the community. Close personal contact with infectious blood or other body fluids or tissue (see Chapter 23) leads to human-to-human transmission. • Microbiologists first isolated Ebola viruses from humans during earlier outbreaks in DROC in 1976. (The virus is named after the Democratic Republic of the Congo's Ebola River.) In 2014, the World Health organization declared, an Ebola virus outbreak in West Africa. In 1989 and 1996, outbreaks among monkeys imported into the United States from the Philippines were caused by another Ebola virus but were not associated with human disease. • Recorded cases of Marburg virus, another hemorrhagic fever virus, are rare. The first cases were laboratory workers in Europe who handled African green monkeys from Uganda. Four outbreaks were identified in Africa between 1975 and 1998, involving 2 to 154 people with 56% mortality. In 2004, an outbreak killed 227 people. African fruit bats are the natural reservoir for the Marburg virus, and microbiologists suspect that bats are the reservoir for EHF. • In 1993, an outbreak of cryptosporidiosis (KRIP-tō-sporiʹdē- Ō-sis) transmitted through the public water supply in Milwaukee, Wisconsin, resulted in diarrheal illness in an estimated 403,000 persons. The microorganism responsible for this outbreak was the protozoan Cryptosporidium (KRIP-tō-sporiʹdē- um). First reported as a cause of human disease in 1976, it is responsible for up to 30% of the diarrheal illness in developing countries. In the United States, transmission has occurred via drinking water, swimming pools, and contaminated hospital supplies. • AIDS (acquired immunodeficiency syndrome) first came to public attention in 1981 with reports from Los Angeles that a few young homosexual men had died of a previously rare type of pneumonia known as Pneumocystis (noo-mō-SIS-tis) pneumonia. These men had experienced a severe weakening of the immune system, which normally fights infectious diseases. Soon these cases were correlated with an unusual number of occurrences of a rare form of cancer, Kaposi's sarcoma, among young homosexual men. Similar increases in such rare diseases were found among hemophiliacs and intravenous drug users. • Researchers quickly discovered that the cause of AIDS was a previously unknown virus (see Figure 1.1e). The virus, now called human immunodeficiency virus (HIV), destroys CD4+ T cells, one type of white blood cell important to immune system defenses. Sickness and death result from microorganisms or cancerous cells that might otherwise have been defeated by the body's natural defenses. So far, the disease has been inevitably fatal once symptoms develop. • By studying disease patterns, medical researchers found that HIV could be spread through sexual intercourse, by contaminated needles, from infected mothers to their newborns via breast milk, and by blood transfusions—in short, by the transmission from one person to another. Since 1985, blood used for transfusions has been carefully checked for the presence of HIV, and it is now quite unlikely that the virus can be spread by this means. • By the end of 2013, over 1 million people in the United States were living with AIDS. About 50,000 Americans become infected and 18,000 die each year. As of 2011, health officials estimated that 1.8 million Americans have HIV infection. In 2013, the World Health Organization (WHO) estimated that over 35 million people worldwide are living with HIV/AIDS and that 6000 new infections occur every day. • Since 1994, new treatments have extended the life span of people with AIDS. The majority of individuals with AIDS are in the sexually active age group. Because heterosexual partners of AIDS sufferers are at high risk of infection, public health officials are concerned that even more women and minorities will contract AIDS. In 1997, HIV diagnoses began increasing among women and minorities. Among the AIDS cases reported in 2009, 26% were women, and 49% were African American. • In the months and years to come, scientists will continue to apply microbiological techniques to help them learn more about the structure of the deadly HIV, how it is transmitted, how it grows in cells and causes disease, how drugs can be directed against it, and whether an effective vaccine can be developed. Public health officials have also focused on prevention through education. • AIDS poses one of this century's most formidable health threats, but it is not the first serious epidemic of a sexually transmitted infection. Syphilis was also once a fatal epidemic disease. As recently as 1941, syphilis caused an estimated 14,000 deaths per year in the United States. With few drugs available for treatment and no vaccines to prevent it, efforts to control the disease focused mainly on altering sexual behavior and on the use of condoms. The eventual development of drugs to treat syphilis contributed significantly to preventing the spread of the disease. According to the Centers for Disease Control and Prevention (CDC), reported cases of syphilis dropped from a record high of 575,000 in 1943 to an all-time low of 5979 cases in 2004. Since then, however, the number of cases has been increasing. • Just as microbiological techniques helped researchers in the fight against syphilis and smallpox, they will help scientists discover the causes of new emerging infectious diseases in the twenty-first century. Undoubtedly there will be new diseases. Ebola virus and Influenzavirus are examples of viruses that may be changing their abilities to infect different host species. Emerging infectious diseases will be discussed further in Chapter 14 on page 405. • Infectious diseases may reemerge because of antibiotic resistance (see the Clinical Focus box in Chapter 26 on page 756) and through the use of microorganisms as weapons. (See the Clinical Focus box in Chapter 23 on page 645.) The breakdown of public health measures for previously controlled infections has resulted in unexpected cases of tuberculosis, whooping cough, and diphtheria (see Chapter 24).

11. Pasteur found that yeasts ferment sugars to alcohol and that bacteria can oxidize the alcohol to acetic acid.

Fermentation • One of the key steps that established the relationship between microorganisms and disease occurred when a group of French merchants asked Pasteur to find out why wine and beer soured. o They hoped to develop a method that would prevent spoilage when those beverages were shipped long distances. o At the time, many scientists believed that air converted the sugars in these fluids into alcohol. o Pasteur found instead that microorganisms called yeasts convert the sugars to alcohol in the absence of air. o This process, called fermentation (see Chapter 5, page 127), is used to make wine and beer. o Souring and spoilage are caused by different microorganisms, called bacteria. In the presence of air, bacteria change the alcohol into vinegar (acetic acid).

4. Francesco Redi demonstrated that maggots appear on decaying meat only when flies are able to lay eggs on the meat (1668).

Francesco Redi - maggots from on decaying meat only when after flies lay eggs on meat. • Physician Francesco Redi set out in 1668 to demonstrate that maggots did not generate spontaneously. o Redi filled two jars with decaying meat. o The first was left unsealed, allowing flies to lay eggs on the meat, which developed into larvae. o The second jar was sealed, and because the flies could not get inside, no maggots appeared. o Still, Redi's antagonists were not convinced; they claimed that fresh air was needed for spontaneous generation. o So Redi set up a second experiment, in which he covered a jar with a fine net instead of sealing it. o No larvae appeared in the gauzecovered jar, even though air was present. • Redi's results were a serious blow to the long-held belief that large forms of life could arise from nonlife. o However, many scientists still believed that small organisms, such as van Leeuwenhoek's "animalcules," were simple enough to generate from nonliving materials.

6. Lazzaro Spallanzani repeated Needham's experiments and suggested that Needham's results were due to microorganisms in the air entering his broth (1765).

Lazzaro Spallanzani repeated Needham's experiments. • Twenty years later, Lazzaro Spallanzani suggested that microorganisms from the air probably entered Needham's solutions after they were boiled. o Spallanzani showed that nutrient fluids heated after being sealed in a flask did not develop microbial growth. o Needham responded by claiming the "vital force" necessary for spontaneous generation had been destroyed by the heat and was kept out of the flasks by the seals. • Spallanzani's observations were also criticized on the grounds that there was not enough oxygen in the sealed flasks to support microbial life.

Microbes in Our Lives (p. 2)

Learning Objective 1-1 List several ways in which microbes affect our lives. Check Your Understanding ✓ Describe some of the destructive and beneficial actions of microbes. 1-1*

Microbes and Human Welfare (pp. 13-15)

Learning Objectives 1-14 List at least four beneficial activities of microorganisms. 1-15 Name two examples of biotechnology that use recombinant DNA technology and two examples that do not. Check Your Understanding ✓ Name two beneficial uses of bacteria. 1-14 ✓ Differentiate biotechnology from recombinant DNA technology. 1-15

9. Fungal Nutrition - obtain nutrients by absorbing organic material from their environment

Fungal Nutrition. • They obtain nourishment by absorbing solutions of organic material from their environment—whether soil, seawater, freshwater, or an animal or plant host

8. Fungi (mushrooms, molds, and yeasts) - eukaryotic cells (w/ true nucleus) - Most are multicellular

Fungi (singular: fungus) • Eukaryotes (DNA in nucleus) • May be unicellular or multicellular • True fungi have cell walls (chitin) • Fungi can reproduce sexually or asexually. • Large multicellular fungi, such as mushrooms, o may look somewhat like plants, but cannot carry out photosynthesis • Unicellular forms of fungi, yeasts o are oval microorganisms that are larger than bacteria • The most typical fungi are molds o Molds form visible masses called mycelia - composed of long filaments (hyphae) that branch and intertwine - cottony growths on moldy bread and fruit are mycelia • Organisms called slime molds have characteristics of both fungi and amebae

Types of Microorganisms (pp. 3-5)

Here is an overview of the main types of microorganisms. (The classification and identification of microorganisms are discussed in Chapter 10.) Check Your Understanding ✓ Which groups of microbes are prokaryotes? Which are eukaryotes? 1-3

The First Observations (p. 6) 1. Hooke's observations laid the groundwork for development of the cell theory, the concept that all living things are composed of cells.

Hooke's observations laid the groundwork for development of the cell theory • In 1665, after observing a thin slice of cork through a crude microscope, Englishman Robert Hooke reported that life's smallest structural units were "little boxes," or "cells." • Using his improved microscope, Hooke later saw individual cells. • Hooke's discovery marked the beginning of the cell theory—the theory that all living things are composed of cells.

Microbes and Human Disease (pp. 15-19)

Learning Objectives 1-16 Define normal microbiota and resistance. 1-17 Define biofilm. 1-18 Define emerging infectious disease. Check Your Understanding ✓ Differentiate normal microbiota and infectious disease. 1-16 ✓ Why are biofilms important? 1-17 ✓ What factors contribute to the emergence of an infectious disease? 1-18 The diseases we have mentioned are caused by viruses, bacteria, protozoa, and prions—types of microorganisms. • This book introduces you to the enormous variety of microscopic organisms. • It shows you how microbiologists use specific techniques and procedures to study the microbes that cause such diseases as AIDS and diarrhea—and diseases that have yet to be discovered. • You will also learn how the body responds to microbial infection and how certain drugs combat microbial diseases. • Finally, you will learn about the many beneficial roles that microbes play in the world around us.

26. The study of AIDS, analysis of the action of interferons, and the development of new vaccines are among the current research interests in immunology.

Immunology • Immunology is the study of immunity. • Knowledge about the immune system has accumulated steadily and expanded rapidly. • Vaccines are now available for numerous diseases, including measles, rubella (German measles), mumps, chickenpox, pneumococcal pneumonia, tetanus, tuberculosis, influenza, whooping cough, polio, and hepatitis B. • The smallpox vaccine was so effective that the disease has been eliminated. • Public health officials estimate that polio will be eradicated within a few years because of the polio vaccine. • A major advance in immunology occurred in 1933, when Rebecca Lancefield (Figure 1.7) proposed that streptococci be classified according to serotypes (variants within a species) based on certain components in the cell walls of the bacteria. • Streptococci are responsible for a variety of diseases, such as sore throat (strep throat), streptococcal toxic shock, and septicemia (blood poisoning). • In 1960, interferons, substances generated by the body's own immune system, were discovered. • Interferons inhibit replication of viruses and have triggered considerable research related to the treatment of viral diseases and cancer. • One of today's biggest challenges for immunologists is learning how the immune system might be stimulated to ward off the virus responsible for AIDS, a disease that destroys the immune system.

4. An infectious disease is one in which pathogens invade a susceptible host.

Infectious Diseases • An infectious disease is a disease in which pathogens invade a susceptible host, such as a human or an animal. • In the process, the pathogen carries out at least part of its life cycle inside the host, and disease frequently results. • By the end of World War II, many people believed that infectious diseases were under control. • They thought malaria would be eradicated through the use of the insecticide DDT to kill mosquitoes, that a vaccine would prevent diphtheria, and that improved sanitation measures would help prevent cholera transmission. • Malaria is far from eliminated. • Since 1986, local outbreaks have been identified in New Jersey, California, Florida, New York, and Texas, and the disease infects 300 million people worldwide. In 1994, diphtheria appeared in the United States, brought by travelers from the newly independent states of the former Soviet Union, which were experiencing a massive diphtheria epidemic. • The epidemic was brought under control in 1998. Cholera outbreaks still occur in less-developed parts of the world.

4. Bacteria that cause diseases in insects are being used as biological controls of insect pests. Biological controls are specific for the pest and do not harm the environment.

Insect Pest Control by Microorganisms • Besides spreading diseases, insects can cause devastating crop damage. • Insect pest control is therefore important for both agriculture and the prevention of human disease. • The bacterium Bacillus thuringiensis has been used extensively in the United States to control such pests as alfalfa caterpillars, bollworms, corn borers, cabbageworms, tobacco budworms, and fruit tree leaf rollers. • It is incorporated into a dusting powder that is applied to the crops these insects eat. • The bacteria produce protein crystals that are toxic to the digestive systems of the insects. • The toxin gene also has been inserted into some plants to make them insect resistant. • By using microbial rather than chemical insect control, farmers can avoid harming the environment. • Many chemical insecticides, such as DDT, remain in the soil as toxic pollutants and are eventually incorporated into the food chain.

A Brief History of Microbiology (pp. 6-13)

Learning Objectives 1-5 Explain the importance of observations made by Hooke and van Leeuwenhoek. 1-6 Compare spontaneous generation and biogenesis. 1-7 Identify the contributions to microbiology made by Needham, Spallanzani, Virchow, and Pasteur. 1-8 Explain how Pasteur's work influenced Lister and Koch. 1-9 Identify the importance of Koch's postulates. 1-10 Identify the importance of Jenner's work. 1-11 Identify the contributions to microbiology made by Ehrlich and Fleming. 1-12 Define bacteriology, mycology, parasitology, immunology, and virology. 1-13 Explain the importance of microbial genetics and molecular biology. Bacterial ancestors were the first living cells to appear on Earth. For most of human history, people knew little about the true causes, transmission, and effective treatment of disease. Let's look now at some key developments in microbiology that have spurred the field to its current technological state. Check Your Understanding ✓ What is the cell theory? 1-5 Check Your Understanding ✓ What evidence supported spontaneous generation? 1-6 ✓ How was spontaneous generation disproved? 1-7 Check Your Understanding ✓ Summarize in your own words the germ theory of disease. 1-8 ✓ What is the importance of Koch's postulates? 1-9 ✓ What is the significance of Jenner's discovery? 1-10 Check Your Understanding ✓ What was Ehrlich's "magic bullet"? 1-11 Check Your Understanding ✓ Define bacteriology, mycology, parasitology, immunology, and virology. 1-12 ✓ Differentiate microbial genetics from molecular biology. 1-13

8. Louis Pasteur demonstrated that microorganisms are in the air everywhere and offered proof of biogenesis (1861).

Louis Pasteur - demonstrated - microorganisms are in the air everywhere - proof of biogenesis (1861). • Pasteur demonstrated that microorganisms are present in the air and can contaminate sterile solutions, but that air itself does not create microbes. o He filled several short-necked flasks with beef broth and then boiled their contents. o Some were then left open and allowed to cool. o In a few days, these flasks were found to be contaminated with microbes. o The other flasks, sealed after boiling, were free of microorganisms. o From these results, Pasteur reasoned that microbes in the air were the agents responsible for contaminating nonliving matter. • Pasteur next placed broth in open-ended, long-necked flasks and bent the necks into S-shaped curves (Figure 1.3). o The contents of these flasks were then boiled and cooled. o The broth in the flasks did not decay and showed no signs of life, even after months. o Pasteur's unique design allowed air to pass into the flask, but the curved neck trapped any airborne microorganisms that might contaminate the broth. o (Some of these original vessels are still on display at the Pasteur Institute in Paris. They have been sealed but, like the flask in Figure 1.3, show no sign of contamination more than 100 years later.)

1. Everyone has microorganisms in and on the body; these make up the normal microbiota, or flora.

Microbes and Human Disease Normal Microbiota • We all live from birth until death in a world filled with microbes, and we all have a variety of microorganisms on and inside our bodies. • These microorganisms make up our normal microbiota, or flora* (Figure 1.8). • The normal microbiota not only do us no harm, but in some cases can actually benefit us. • For example, some normal microbiota protect us against disease by preventing the overgrowth of harmful microbes, and others produce useful substances such as vitamin K and some B vitamins. • Unfortunately, under some circumstances normal microbiota can make us sick or infect people we contact. • For instance, when some normal microbiota leave their habitat, they can cause disease.

27. New techniques in molecular biology and electron microscopy have provided tools for advancing our knowledge of virology.

Virology • The study of viruses, virology, originated during the Golden Age of Microbiology. • In 1892, Dmitri Iwanowski reported that the organism that caused mosaic disease of tobacco was so small that it passed through filters fine enough to stop all known bacteria. • At the time, Iwanowski was not aware that the organism in question was a virus. • In 1935, Wendell Stanley demonstrated that the organism, called tobacco mosaic virus (TMV), was fundamentally different from other microbes and so simple and homogeneous that it could be crystallized like a chemical compound. • Stanley's work facilitated the study of viral structure and chemistry. • Since the development of the electron microscope in the 1940s, microbiologists have been able to observe the structure of viruses in detail, and today much is known about their structure and activity.

1. Microorganisms degrade dead plants and animals and recycle chemical elements to be used by living plants and animals.

Microbes and Human Welfare • As mentioned earlier, only a minority of all microorganisms are pathogenic. • Microbes that cause food spoilage, such as soft spots on fruits and vegetables, decomposition of meats, and rancidity of fats and oils, are also a minority. • The vast majority of microbes benefit humans, other animals, and plants in many ways. • For example, microbes produce methane and ethanol that can be used as alternative fuels to generate electricity and power vehicles. • Biotechnology companies are using bacterial enzymes to break down plant cellulose so that yeast can metabolize the resulting simple sugars and produce ethanol. • The following sections outline some of these beneficial activities. In later chapters, we will discuss these activities in greater detail. Recycling Vital Elements • Discoveries made by two microbiologists in the 1880s have formed the basis for today's understanding of the biogeochemical cycles that support life on Earth. • Martinus Beijerinck and Sergei Winogradsky were the first to show how bacteria help recycle vital elements between the soil and the atmosphere. • Microbial ecology, the study of the relationship between microorganisms and their environment, originated with the work of these scientists. • Today, microbial ecology has branched out and includes the study of how microbial populations interact with plants and animals in various environments. • Among the concerns of microbial ecologists are water pollution and toxic chemicals in the environment. • The chemical elements carbon, nitrogen, oxygen, sulfur, and phosphorus are essential for life and abundant, but not necessarily in forms that organisms can use. • Microorganisms are primarily responsible for converting these elements into forms that plants and animals can use. • Microorganisms, especially bacteria and fungi, return carbon dioxide to the atmosphere when they decompose organic wastes and dead plants and animals. • Algae, cyanobacteria, and higher plants use the carbon dioxide during photosynthesis to produce carbohydrates for animals, fungi, and bacteria. • Nitrogen is abundant in the atmosphere but in that form is not usable by plants and animals. • Only bacteria can naturally convert atmospheric nitrogen to a form available to plants and animals.

25. Microbiologists are using genomics, the study of all of an organism's genes, to classify bacteria, fungi, and protozoa.

Microbiologists are using genomics, the study of all of an organism's genes, to classify bacteria, fungi, and protozoa. • Bacteriology, mycology, and parasitology are currently going through a "golden age" of classification. • Recent advances in genomics, the study of all of an organism's genes, have allowed scientists to classify bacteria and fungi according to their genetic relationships with other bacteria, fungi, and protozoa. • These microorganisms were originally classified according to a limited number of visible characteristics.

5. Using microbes to make products such as foods and chemicals is called biotechnology.

Modern Biotechnology and Recombinant DNA Technology • Earlier, we touched on the commercial use of microorganisms to produce some common foods and chemicals. • Such practical applications of microbiology are called biotechnology. • Although biotechnology has been used in some form for centuries, techniques have become much more sophisticated in the past few decades. • In the last several years, biotechnology has undergone a revolution through the advent of recombinant DNA technology to expand the potential of bacteria, viruses, and yeast and other fungi as miniature biochemical factories. • Cultured plant and animal cells, as well as intact plants and animals, are also used as recombinant cells and organisms.

Modern Developments in Microbiology (pp. 11-13) 24. Bacteriology is the study of bacteria, mycology is the study of fungi, and parasitology is the study of parasitic protozoa and worms.

Modern Developments in Microbiology • The quest to solve drug resistance, identify viruses, and develop vaccines requires sophisticated research techniques and correlated studies that were never dreamed of in the days of Koch and Pasteur. • The groundwork laid during the Golden Age of Microbiology provided the basis for several monumental achievements in the years following (Table 1.2). o New branches of microbiology were developed, including immunology and virology. Most recently, the development of a set of new methods called recombinant DNA technology has revolutionized research and practical applications in all areas of microbiology. Bacteriology, Mycology, and Parasitology Bacteriology, the study of bacteria, began with van Leeuwenhoek's first examination of tooth scrapings. • New pathogenic bacteria are still discovered regularly. Many bacteriologists, like Pasteur, look at the roles of bacteria in food and the environment. One intriguing discovery came in 1997, when Heide Schulz discovered a bacterium large enough to be seen with the unaided eye (0.2 mm wide). This bacterium, named Thiomargarita namibiensis (THĪ-ō-mar-garʹē-tah nahʹmib-ē-EN-sis), lives in the mud on the African coast. Thiomargarita is unusual because of its size and its ecological niche. The bacterium consumes hydrogen sulfide, which would be toxic to mud-dwelling animals (Figure 11.28, page 315). Mycology, the study of fungi, includes medical, agricultural, and ecological branches. • Fungal infection rates have been rising during the past decade, accounting for 10% of hospital-acquired infections. Climatic and environmental changes (severe drought) are thought to account for the tenfold increase in Coccidioides immitis (KOK-sid-ē-oi-dēz IM-mi-tis) infections in California. New techniques for diagnosing and treating fungal infections are currently being investigated. Parasitology is the study of protozoa and parasitic worms. • Because many parasitic worms are large enough to be seen with the unaided eye, they have been known for thousands of years. It has been speculated that the medical symbol, the rod of Asclepius, represents the removal of parasitic guinea worms (Figure 1.6). Asclepius was a Greek physician who practiced about 1200 B.C. and was deified as the god of medicine. • The clearing of rain forests has exposed laborers to previously undiscovered parasites. Parasitic diseases unknown until recently are also being found in patients whose immune systems have been suppressed by organ transplants, cancer chemotherapy, or AIDS.

18. Modern vaccines are prepared from living avirulent microorganisms or killed pathogens, from isolated components of pathogens, and by recombinant DNA techniques.

Modern vaccines are prepared from living avirulent microorganisms or killed pathogens, from isolated components of pathogens, and by recombinant DNA techniques. • Some vaccines are still produced from avirulent microbial strains that stimulate immunity to the related virulent strain. o Other vaccines are made from killed virulent microbes, from isolated components of virulent microorganisms, or by genetic engineering techniques.

16. Multicellular Animal Parasites - - flatworms and roundworms, collectively called helminths

Multicellular Animal Parasites • multicellular animal parasites - not microorganisms, they are of medical importance • eukaryotes • two major groups of parasitic worms are the collectively called helminths o flatworms o roundworms

9. Pasteur's discoveries led to the development of aseptic techniques used in laboratory and medical procedures to prevent contamination by microorganisms.

Pasteur - Aseptic techniques to prevent contamination in laboratory and medical procedures. • Pasteur showed that microorganisms can be present in nonliving matter—on solids, in liquids, and in the air. o Furthermore, he demonstrated conclusively that microbial life can be destroyed by heat and that methods can be devised to block the access of airborne microorganisms to nutrient environments. o These discoveries form the basis of aseptic techniques, procedures that prevent contamination by unwanted microorganisms, which are now the standard practice in laboratory and many medical procedures. o Modern aseptic techniques are among the first and most important concepts that a beginning microbiologist learns. • Pasteur's work provided evidence that microorganisms cannot originate from mystical forces present in nonliving materials. o Rather, any appearance of "spontaneous" life in nonliving solutions can be attributed to microorganisms that were already present in the air or in the fluids themselves. o Scientists now believe that a form of spontaneous generation probably did occur on the primitive Earth when life first began, but they agree that this does not happen under today's environmental conditions.

12. A heating process called pasteurization is used to kill bacteria in some alcoholic beverages and milk.

Pasteurization • Pasteur's solution to the spoilage problem was to heat the beer and wine just enough to kill most of the bacteria that caused the spoilage. o The process, called pasteurization, is now commonly used to reduce spoilage and kill potentially harmful bacteria in milk as well as in some alcoholic drinks.

10. Protozoa - unicellular eukaryotes

Protozoa (singular: protozoan) • unicellular eukaryotic microbes • move by pseudopods, flagella, or cilia. o Amebae - move by using pseudopods (false feet) - cytoplasmic extensions o Others - have flagella or cilia - for locomotion • can reproduce sexually or asexually

11. Protozoa Nutrition - obtain nourishment by absorption or ingestion through specialized structures

Protozoa Nutrition. • Have a variety of shapes - live either as free entities or as parasites (organisms that derive nutrients from living hosts) that absorb or ingest organic compounds from their environment • Some protozoa, such as Euglena, are photosynthetic o use light as a source of energy o carbon dioxide as their chief source of carbon to produce sugars

14. Viruses - noncellular entities - parasites of cells

Viruses • very different from the other microbial groups - acellular • so small that most can be seen only with an electron microscope • reproduce only by using the cellular machinery of other organisms • considered to be living only when they multiply within host cells they infect o parasites of other forms of life • not considered to be living because they are inert outside living hosts

15. Viruses consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat. An envelope may surround the coat.

Viruses - nucleic acid core (DNA or RNA) - protein coat - envelope Structurally very simple • virus particle contains • a core made of only one type of nucleic acid, either DNA or RNA o surrounded by a protein coat - sometimes encased by a lipid membrane (envelope) • in contrast - All living cells have RNA and DNA, can carry out chemical reactions, and can reproduce as self-sufficient units

28. The development of recombinant DNA technology has helped advance all areas of microbiology.

Recombinant DNA Technology • Microorganisms can now be genetically modified to manufacture large amounts of human hormones and other urgently needed medical substances. • In the late 1960s, Paul Berg showed that fragments of human or animal DNA (genes) that code for important proteins can be attached to bacterial DNA. • The resulting hybrid was the first example of recombinant DNA. • Recombinant DNA (rDNA) technology inserts recombinant DNA into bacteria (or other microbes) to make large quantities of a desired protein. • This field combines elements from two other areas of study, including microbial genetics, which studies the mechanisms by which microorganisms inherit traits, and molecular biology, which looks at how genetic information is carried in molecules of DNA and how DNA directs the synthesis of proteins. • Although molecular biology encompasses all organisms, much of our knowledge of how genes determine specific traits has been revealed through experiments with bacteria. • Unicellular organisms, primarily bacteria, have several advantages for genetic and biochemical research. • Bacteria are less complex than plants and animals, and the life cycles of many bacteria last less than an hour, so scientists can cultivate very large numbers of bacteria for study in a relatively short time. • Once science turned to the study of unicellular life, rapid progress was made in genetics. • In the 1940s, George W. Beadle and Edward L. Tatum demonstrated the relationship between genes and enzymes; DNA was established as the hereditary material by Oswald Avery, Colin MacLeod, and Maclyn McCarty; and Joshua Lederberg and Edward L. Tatum discovered that genetic material could be transferred from one bacterium to another by a process called conjugation. • Then in the 1950s, James Watson and Francis Crick proposed a model for the structure and replication of DNA. • The early 1960s also witnessed a further explosion of discoveries relating to the way DNA controls protein synthesis. • François Jacob and Jacques Monod discovered messenger RNA (ribonucleic acid), a chemical involved in protein synthesis, and later they made the first major discoveries about the regulation of gene function in bacteria. • During the same period, scientists were able to break the genetic code and thus understand how the information for protein synthesis in messenger RNA is translated into the amino acid sequence for making proteins.

23. Researchers are tackling the problem of drug-resistant microbes.

Researchers are tackling the problem of drug-resistant microbes. • Over the years, more and more microbes also developed resistance to antibiotics that were once very effective against them. o Drug resistance results from genetic changes in microbes that enables them to tolerate a certain amount of an antibiotic that would normally inhibit them (see the box in Chapter 26, page 756). o For example, a microbe might produce enzymes that inactivate antibiotics, or a microbe might undergo changes to its surface that prevent an antibiotic from attaching to it or entering it. • The recent appearance of vancomycin-resistant Staphylococcus aureus and Enterococcus faecalis has alarmed health care professionals because it indicates that some previously treatable bacterial infections may soon be impossible to treat with antibiotics.

15. Robert Koch proved that microorganisms cause disease. He used a sequence of procedures, now called Koch's postulates (1876), that are used today to prove that a particular microorganism causes a particular disease.

Robert Koch - proved that microorganisms cause disease - Koch's postulates (1876). • The first proof that bacteria actually cause disease came from Robert Koch in 1876. o Koch, a German physician, was Pasteur's rival in the race to discover the cause of anthrax, a disease that was destroying cattle and sheep in Europe. o Koch discovered rourod- shaped bacteria now known as Bacillus anthracis in the blood of cattle that had died of anthrax. o He cultured the bacteria on nutrients and then injected samples of the culture into healthy animals. o When these animals became sick and died, Koch isolated the bacteria in their blood and compared them with the originally isolated bacteria. o He found that the two sets of blood cultures contained the same bacteria. • Koch thus established Koch's postulates, a sequence of experimental steps for directly relating a specific microbe to a specific disease (see Figure 14.3, page 395). o During the past 100 years, these same criteria have been invaluable in investigations proving that specific microorganisms cause many diseases. o Koch's postulates, their limitations, and their application to disease will be discussed in greater detail in Chapter 14.

2. Two names - a genus and a specific epithet, both of which are underlined or italicized.

Scientific nomenclature assigns each organism two names— • the genus (plural: genera) - always capitalized • the specific epithet (species name) - not capitalized o Both names are underlined or italicized. o After a scientific name has been mentioned once, it can be abbreviated with the initial of the genus followed by the specific epithet • Scientific names can, among other things, describe an organism, honor a researcher, or identify the habitat of a species. o Staphylococcus aureus, a bacterium commonly found on human skin Staphylo- describes the clustered arrangement of the cells -coccus indicates that they are shaped like spheres The specific epithet, aureus, is Latin for golden, the color of many colonies o The genus of the bacterium Escherichia coli is named for a scientist, Theodor Escherich, whereas its specific epithet, coli, reminds us that E. coli live in the colon, or large intestine.

2. Bacteria are used to decompose organic matter in sewage.

Sewage Treatment: Using Microbes to Recycle Water • Our society's growing awareness of the need to preserve the environment has made people more conscious of the responsibility to recycle precious water and prevent the pollution of rivers and oceans. • One major pollutant is sewage, which consists of human excrement, waste water, industrial wastes, and surface runoff. • Sewage is about 99.9% water, with a few hundredths of 1% suspended solids. • The remainder is a variety of dissolved materials. • Sewage treatment plants remove the undesirable materials and harmful microorganisms. • Treatments combine various physical processes with the action of beneficial microbes. • Large solids such as paper, wood, glass, gravel, and plastic are removed from sewage; left behind are liquid and organic materials that bacteria convert into such by-products as carbon dioxide, nitrates, phosphates, sulfates, ammonia, hydrogen sulfide, and methane. • (We will discuss sewage treatment in detail in Chapter 27.)

The Birth of Modern Chemotherapy: Dreams of a "Magic Bullet" (pp. 10-11) 19. Chemotherapy is the chemical treatment of a disease.

The Birth of Modern Chemotherapy: Dreams of a "Magic Bullet" • After the relationship between microorganisms and disease was established, medical microbiologists next focused on the search for substances that could destroy pathogenic microorganisms without damaging the infected animal or human. • Treatment of disease by using chemical substances is called chemotherapy. • (The term also commonly refers to chemical treatment of noninfectious diseases, such as cancer.)

21. Paul Ehrlich introduced an arsenic-containing chemical called salvarsan to treat syphilis (1910).

The First Synthetic Drugs - Paul Ehrlich introduced an arsenic-containing chemical called salvarsan to treat syphilis (1910). • Paul Ehrlich was the imaginative thinker who fired the first shot in the chemotherapy revolution. o As a medical student, Ehrlich speculated about a "magic bullet" that could hunt down and destroy a pathogen without harming the infected host. In 1910, after testing hundreds of substances, he found a chemotherapeutic agent called salvarsan, an arsenic derivative effective against syphilis. o The agent was named salvarsan because it was considered to offer salvation from syphilis and it contained arsenic. o Before this discovery, the only known chemical in Europe's medical arsenal was an extract from the bark of a South American tree, quinine, which had been used by Spanish conquistadors to treat malaria. • By the late 1930s, researchers had developed several other synthetic drugs that could destroy microorganisms. o Most of these drugs were derivatives of dyes. This came about because the dyes synthesized and manufactured for fabrics were rourod tinely tested for antimicrobial qualities by microbiologists looking for a "magic bullet." In addition, sulfonamides (sulfa drugs) were synthesized at about the same time.

13. Agostino Bassi (1835) and Pasteur (1865) showed a causal relationship between microorganisms and disease.

The Germ Theory of Disease - Agostino Bassi (1835) and Pasteur (1865) • Before the time of Pasteur, effective treatments for many diseases were discovered by trial and error, but the causes of the diseases were unknown. o The realization that yeasts play a crucial role in fermentation was the first link between the activity of a microorganism and physical and chemical changes in organic materials. o This discovery alerted scientists to the possibility that microorganisms might have similar relationships with plants and animals—specifically, that microorganisms might cause disease. o This idea was known as the germ theory of disease. • The germ theory met great resistance at first because for centuries disease was believed to be punishment for an individual's crimes or misdeeds. o When the inhabitants of an entire village became ill, people often blamed the disease on demons appearing as foul odors from sewage or on poisonous vapors from swamps. o Most people born in Pasteur's time found it inconceivable that "invisible" microbes could travel through the air to infect plants and animals or remain on clothing and bedding to be transmitted from one person to another. o Despite these doubts, scientists gradually accumulated the information needed to support the new germ theory. • In 1865, Pasteur was called upon to help fight silkworm disease, which was ruining the silk industry in Europe. o Decades earlier amateur microscopist Agostino Bassi had proved that another silkworm disease was caused by a fungus. o Using data provided by Bassi, Pasteur found that the more recent infection was caused by a protozoan, and he developed a method for recognizing afflicted silkworm moths.

16. In 1798, Edward Jenner demonstrated that inoculation with cowpox material provides humans with immunity to smallpox.

Vaccination - (1798) Edward Jenner - inoculation with cowpox provides immunity to smallpox. • Often a treatment or preventive procedure is developed before scientists know why it works. o The smallpox vaccine is an example. o Almost 70 years before Koch established that a specific microorganism causes anthrax, Edward Jenner, a young British physician, embarked on an experiment to find a way to protect people from smallpox. o The disease periodically swept through Europe, killing thousands, and it wiped out 90% of the Native Americans on the East Coast when European settlers first brought the infection to the New World. • When a young milkmaid informed Jenner that she couldn't get smallpox because she already had been sick from cowpox—a much milder disease—he decided to put the girl's story to the test. o First Jenner collected scrapings from cowpox blisters. o Then he inoculated a healthy 8-year-old volunteer with the cowpox material by scratching the person's arm with a pox-contaminated needle. o The scratch turned into a raised bump. o In a few days, the volunteer became mildly sick but recovered and never again contracted either cowpox or smallpox. o The protection from disease provided by vaccination (or by recovery from the disease itself) is called immunity. o We will discuss the mechanisms of immunity in Chapter 17.

7. In gene therapy, viruses are used to carry replacements for defective or missing genes into human cells.

• A very exciting and important outcome of recombinant DNA techniques is gene therapy—inserting a missing gene or replacing a defective one in human cells. • This technique uses a harmless virus to carry the missing or new gene into certain host cells, where the gene is picked up and inserted into the appropriate chromosome. • Since 1990, gene therapy has been used to treat patients with adenosine deaminase (ADA) deficiency, a cause of severe combined immunodeficiency disease (SCID), in which cells of the immune system are inactive or missing; Duchenne's muscular dystrophy, a muscle-destroying disease; cystic fibrosis, a disease of the secreting portions of the respiratory passages, pancreas, salivary glands, and sweat glands; and LDL-receptor deficiency, a condition in which low-density lipoprotein (LDL) receptors are defective and LDL cannot enter cells. • The LDL remains in the blood in high concentrations and leads to fatty plaque formation in blood vessels, increasing the risk of atherosclerosis and coronary heart disease. • Results of gene therapy are still being evaluated. • Other genetic diseases may also be treatable by gene therapy in the future, including hemophilia, an inability of the blood to clot normally; diabetes, elevated blood sugar levels; and sickle cell disease, an abnormal kind of hemoglobin.

8. Genetically modified bacteria are used in agriculture to protect plants from frost and insects and to improve the shelf life of produce.

• Beyond medical applications, recombinant DNA techniques have also been applied to agriculture. • For example, genetically altered strains of bacteria have been developed to protect fruit against frost damage, and bacteria are being modified to control insects that damage crops. • Recombinant DNA has also been used to improve the appearance, flavor, and shelf life of fruits and vegetables. • Potential agricultural uses of recombinant DNA include drought resistance, resistance to insects and microbial diseases, and increased temperature tolerance in crops.

20. Two types of chemotherapeutic agents are synthetic drugs (chemically prepared in the laboratory) and antibiotics (substances produced naturally by bacteria and fungi that inhibit the growth of bacteria).

• Chemicals produced naturally by bacteria and fungi to act against other microorganisms are called antibiotics. • Chemotherapeutic agents prepared from chemicals in the laboratory are called synthetic drugs. • The success of chemotherapy is based on the fact that some chemicals are more poisonous to microorganisms than to the hosts infected by the microbes.

3. Some microorganisms live in humans and other animals and are needed to maintain good health.

• Humans and many other animals depend on the microbes in their intestines for o digestion and the o synthesis of some vitamins that their bodies require, including some B vitamins for metabolism and vitamin K for blood clotting

1. - microorganisms - living things too small to be seen with the unaided eye are called

• Microbes (microorganisms) o The group includes bacteria, fungi (yeasts and molds), protozoa, and microscopic algae. o also includes viruses (noncellular entities)

4. Some microorganisms are used to produce foods and chemicals.

• Microorganisms - commercial applications: o Synthesis of chemical products - vitamins, organic acids, enzymes, alcohols, and many drugs e.g., acetone and butanol, and the vitamins B2 (riboflavin) and B12 (cobalamin) o Acetone/Butanol - Chaim Weizmann (1914) - Russian-born chemist in England WWI Aug 1914 - acetone used making cordite (smokeless gunpowder) o Food industry - vinegar, sauerkraut, pickles, soy sauce, cheese, yogurt, bread, alcoholic beverages o Enzymes from microbes - used to synthesize cellulose, digestive aids, drain cleaner, insulin o Microbial enzymes - jeans

Nomenclature (p. 3) 1. Nomenclature system (by Carolus Linnaeus, 1735)

• System of nomenclature for organisms - established by Carolus Linnaeus (1735) • Scientific names - latinized - language used by scholars

6. Using recombinant DNA, bacteria can produce important substances such as proteins, vaccines, and enzymes.

• The applications of recombinant DNA technology are increasing with each passing year. • Recombinant DNA techniques have been used thus far to produce a number of natural proteins, vaccines, and enzymes. • Such substances have great potential for medical use; some of them are described in Table 9.1 on page 242.

2. The disease-producing properties of a species of microbe and the host's resistance are important factors in determining whether a person will contract a disease.

• When is a microbe a welcome part of a healthy human, and when is it a harbinger of disease? • The distinction between health and disease is in large part a balance between the natural defenses of the body and the disease-producing properties of microorganisms. • Whether our bodies overcome the offensive tactics of a particular microbe depends on our resistance—the ability to ward off diseases. • Important resistance is provided by the barrier of the skin, mucous membranes, cilia, stomach acid, and antimicrobial chemicals such as interferons. • Microbes can be destroyed by white blood cells, by the inflammatory response, by fever, and by specific responses of our immune system. • Sometimes, when our natural defenses are not strong enough to overcome an invader, they have to be supplemented by antibiotics or other drugs.

2. Microorganisms - important in maintaining Earth's ecological balance.

• majority of microorganisms maintain the balance of life in our environment o Marine and freshwater microorganisms form the basis of the food chain o Soil microbes help break down wastes and incorporate nitrogen gas from the air into organic compounds, thereby recycling chemical elements among soil, water, living organisms, and air. o Certain microbes play important roles in photosynthesis, a food and oxygen-generating process that is critical to life on Earth.

5. Some microorganisms - pathogenic

• minority of microorganisms are pathogenic o e.g., hospital contamination • microorganisms are ubiquitous o before invention of the microscope- microbes were unknown o disease - cause and transmission not understood o vaccinations and antibiotics - not available