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"page_content": "From boiling thermal hot springs to deep beneath the Antarctic ice, microorganisms can be found almost everywhere on earth in great quantities. Microorganisms (or microbes, as they are also called) are small organisms. Most are so small that they cannot be seen without a microscope. \nMost microorganisms are harmless to humans and, in fact, many are helpful. They play fundamental roles in ecosystems everywhere on earth, forming the backbone of many food webs. People use them to make biofuels, medicines, and even foods. Without microbes, there would be no bread, cheese, or beer. Our bodies are filled with microbes, and our skin alone is home to trillions of them.[1] Some of them we can't live without; others cause diseases that can make us sick or even kill us. \nAlthough much more is known today about microbial life than ever before, the vast majority of this invisible world remains unexplored. Microbiologists continue to identify new ways that microbes benefit and threaten humans. \n1. J. Hulcr et al. \"A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable.\" *PLoS ONE* 7 no. 11 (2012): e47712. doi:10.1371/journal.pone.0047712.\n\n#### **Learning Objectives** \n- Describe how our ancestors improved food with the use of invisible microbes\n- Describe how the causes of sickness and disease were explained in ancient times, prior to the invention of the microscope\n- Describe key historical events associated with the birth of microbiology \nMost people today, even those who know very little about microbiology, are familiar with the concept of microbes, or \"germs,\" and their role in human health. Schoolchildren learn about bacteria, viruses, and other microorganisms, and many even view specimens under a microscope. But a few hundred years ago, before the invention of the microscope, the existence of many types of microbes was impossible to prove. By definition, **microorganisms**, or **microbes**, are very small organisms; many types of microbes are too small to see without a microscope, although some parasites and fungi are visible to the naked eye. \nHumans have been living with—and using—microorganisms for much longer than they have been able to see them. Historical evidence suggests that humans have had some notion of microbial life since prehistoric times and have used that knowledge to develop foods as well as prevent and treat disease. In this section, we will explore some of the historical applications of microbiology as well as the early beginnings of microbiology as a science. \n#### **Fermented Foods and Beverages** \nPeople across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. Discoveries from several archeological sites suggest that even prehistoric people took advantage of fermentation to preserve and enhance the taste of food. Archaeologists studying pottery jars from a Neolithic village in China found that people were making a fermented beverage from rice, honey, and fruit as early as 7000 BC.[2] \nProduction of these foods and beverages requires microbial fermentation, a process that uses bacteria, mold, or yeast to convert sugars (carbohydrates) to alcohol, gases, and organic acids (**[Figure 1.3](#page-25-1)**). While it is likely that people first learned about fermentation by accident—perhaps by drinking old milk that had curdled or old grape juice that had fermented—they later learned to harness the power of fermentation to make products like bread, cheese, and wine. \n \n**Figure 1.3** A microscopic view of *Saccharomyces cerevisiae*, the yeast responsible for making bread rise (left). Yeast is a microorganism. Its cells metabolize the carbohydrates in flour (middle) and produce carbon dioxide, which causes the bread to rise (right). (credit middle: modification of work by Janus Sandsgaard; credit right: modification of work by \"MDreibelbis\"/Flickr) \n2. P.E. McGovern et al. \"Fermented Beverages of Pre- and Proto-Historic China.\" *Proceedings of the National Academy of Sciences of the United States of America* 1 no. 51 (2004):17593–17598. doi:10.1073/pnas.0407921102. \n#### **Clinical Focus** \n#### **Part 1** \nCora, a 41-year-old lawyer and mother of two, has recently been experiencing severe headaches, a high fever, and a stiff neck. Her husband, who has accompanied Cora to see a doctor, reports that Cora also seems confused at times and unusually drowsy. Based on these symptoms, the doctor suspects that Cora may have meningitis, a potentially life-threatening infection of the tissue that surrounds the brain and spinal cord. \nMeningitis has several potential causes. It can be brought on by bacteria, fungi, viruses, or even a reaction to medication or exposure to heavy metals. Although people with viral meningitis usually heal on their own, bacterial and fungal meningitis are quite serious and require treatment. \nCora's doctor orders a lumbar puncture (spinal tap) to take three samples of cerebrospinal fluid (CSF) from around the spinal cord (**[Figure 1.2](#page-26-0)**). The samples will be sent to laboratories in three different departments for testing: clinical chemistry, microbiology, and hematology. The samples will first be visually examined to determine whether the CSF is abnormally colored or cloudy; then the CSF will be examined under a microscope to see if it contains a normal number of red and white blood cells and to check for any abnormal cell types. In the microbiology lab, the specimen will be centrifuged to concentrate any cells in a sediment; this sediment will be smeared on a slide and stained with a Gram stain. Gram staining is a procedure used to differentiate between two different types of bacteria (gram-positive and gram-negative). \nAbout 80% of patients with bacterial meningitis will show bacteria in their CSF with a Gram stain.[3] Cora's Gram stain did not show any bacteria, but her doctor decides to prescribe her antibiotics just in case. Part of the CSF sample will be cultured—put in special dishes to see if bacteria or fungi will grow. It takes some time for most microorganisms to reproduce in sufficient quantities to be detected and analyzed. \n• What types of microorganisms would be killed by antibiotic treatment? \n \n**Figure 1.2** (a) A lumbar puncture is used to take a sample of a patient's cerebrospinal fluid (CSF) for testing. A needle is inserted between two vertebrae of the lower back, called the lumbar region. (b) CSF should be clear, as in this sample. Abnormally cloudy CSF may indicate an infection but must be tested further to confirm the presence of microorganisms. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by James Heilman) \n*Jump to the [next](#page-35-0) Clinical Focus box.*\n\nPrehistoric humans had a very limited understanding of the causes of disease, and various cultures developed different beliefs and explanations. While many believed that illness was punishment for angering the gods or was simply the result of fate, archaeological evidence suggests that prehistoric people attempted to treat illnesses and infections. One example of this is Ötzi the Iceman, a 5300-year-old mummy found frozen in the ice of the Ötzal Alps on the Austrian-Italian border in 1991. Because Ötzi was so well preserved by the ice, researchers discovered that he was infected with the eggs of the parasite *Trichuris trichiura*, which may have caused him to have abdominal pain and anemia. Researchers also found evidence of *Borrelia burgdorferi*, a bacterium that causes Lyme disease.[4] Some researchers think Ötzi may have been trying to treat his infections with the woody fruit of the *Piptoporus betulinus* fungus, which was discovered tied to his belongings.[5] This fungus has both laxative and antibiotic properties. Ötzi was also covered in tattoos that were made by cutting incisions into his skin, filling them with herbs, and then burning the herbs.[6] There is speculation that this may have been another attempt to treat his health ailments.\n\nSeveral ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. This is especially evident in historical attempts to contain the spread of disease. For example, the Bible refers to the practice of quarantining people with leprosy and other diseases, suggesting that people understood that diseases could be communicable. Ironically, while leprosy is communicable, it is also a disease that progresses slowly. This means that people were likely quarantined after they had already spread the disease to others. \nThe ancient Greeks attributed disease to bad air, *mal'aria*, which they called \"miasmatic odors.\" They developed hygiene practices that built on this idea. The Romans also believed in the miasma hypothesis and created a complex sanitation infrastructure to deal with sewage. In Rome, they built aqueducts, which brought fresh water into the city, and a giant sewer, the *Cloaca Maxima*, which carried waste away and into the river Tiber (**[Figure 1.4](#page-28-0)**). Some researchers believe that this infrastructure helped protect the Romans from epidemics of waterborne illnesses. \n3. Rebecca Buxton. \"Examination of Gram Stains of Spinal Fluid—Bacterial Meningitis.\" *American Society for Microbiology*. 2007. http://www.microbelibrary.org/library/gram-stain/3065-examination-of-gram-stains-of-spinal-fluid-bacterial-meningitis \n4. A. Keller et al. \"New Insights into the Tyrolean Iceman's Origin and Phenotype as Inferred by Whole-Genome Sequencing.\" *Nature Communications*, 3 (2012): 698. doi:10.1038/ncomms1701. \n5. L. Capasso. \"5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.\" *The Lancet*, 352 (1998) 9143: 1864. doi: 10.1016/ s0140-6736(05)79939-6. \n6. L. Capasso, L. \"5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.\" *The Lancet*, 352 no. 9143 (1998): 1864. doi: 10.1016/s0140-6736(05)79939-6. \n \n**Figure 1.4** (a) The *Cloaca Maxima*, or \"Greatest Sewer\" (shown in red), ran through ancient Rome. It was an engineering marvel that carried waste away from the city and into the river Tiber. (b) These ancient latrines emptied into the *Cloaca Maxima*. \nEven before the invention of the microscope, some doctors, philosophers, and scientists made great strides in understanding the invisible forces—what we now know as microbes—that can cause infection, disease, and death. \nThe Greek physician Hippocrates (460–370 BC) is considered the \"father of Western medicine\" (**[Figure 1.5](#page-29-0)**). Unlike many of his ancestors and contemporaries, he dismissed the idea that disease was caused by supernatural forces. Instead, he posited that diseases had natural causes from within patients or their environments. Hippocrates and his heirs are believed to have written the *Hippocratic Corpus*, a collection of texts that make up some of the oldest surviving medical books.[7] Hippocrates is also often credited as the author of the Hippocratic Oath, taken by new physicians to pledge their dedication to diagnosing and treating patients without causing harm. \n7. G. Pappas et al. \"Insights Into Infectious Disease in the Era of Hippocrates.\" *International Journal of Infectious Diseases* 12 (2008) 4:347–350. doi: http://dx.doi.org/10.1016/j.ijid.2007.11.003. \nWhile Hippocrates is considered the father of Western medicine, the Greek philosopher and historian Thucydides (460–395 BC) is considered the father of scientific history because he advocated for evidence-based analysis of cause-and-effect reasoning (**[Figure 1.5](#page-29-0)**). Among his most important contributions are his observations regarding the Athenian plague that killed one-third of the population of Athens between 430 and 410 BC. Having survived the epidemic himself, Thucydides made the important observation that survivors did not get re-infected with the disease, even when taking care of actively sick people.[8] This observation shows an early understanding of the concept of immunity. \nMarcus Terentius Varro (116–27 BC) was a prolific Roman writer who was one of the first people to propose the concept that things we cannot see (what we now call microorganisms) can cause disease (**[Figure 1.5](#page-29-0)**). In *Res Rusticae* (*On Farming*), published in 36 BC, he said that \"precautions must also be taken in neighborhood swamps . . . because certain minute creatures [*animalia minuta*] grow there which cannot be seen by the eye, which float in the air and enter the body through the mouth and nose and there cause serious diseases.\"[9] \n \n**Figure 1.5** (a) Hippocrates, the \"father of Western medicine,\" believed that diseases had natural, not supernatural, causes. (b) The historian Thucydides observed that survivors of the Athenian plague were subsequently immune to the infection. (c) Marcus Terentius Varro proposed that disease could be caused by \"certain minute creatures . . . which cannot be seen by the eye.\" (credit c: modification of work by Alessandro Antonelli) \n \n- Give two examples of foods that have historically been produced by humans with the aid of microbes.\n- Explain how historical understandings of disease contributed to attempts to treat and contain disease.\n\nWhile the ancients may have suspected the existence of invisible \"minute creatures,\" it wasn't until the invention of the microscope that their existence was definitively confirmed. While it is unclear who exactly invented the microscope, a Dutch cloth merchant named Antonie van Leeuwenhoek (1632–1723) was the first to develop a lens powerful enough to view microbes. In 1675, using a simple but powerful microscope, Leeuwenhoek was able to observe single-celled organisms, which he described as \"animalcules\" or \"wee little beasties,\" swimming in a drop \n8. Thucydides. *The History of the Peloponnesian War. The Second Book*. 431 BC. Translated by Richard Crawley. http://classics.mit.edu/ Thucydides/pelopwar.2.second.html. \n9. Plinio Prioreschi. *A History of Medicine: Roman Medicine*. Lewiston, NY: Edwin Mellen Press, 1998: p. 215. \nof rain water. From his drawings of these little organisms, we now know he was looking at bacteria and protists. (We will explore Leeuwenhoek's contributions to microscopy further in **[How We See the Invisible World](#page-52-1)**.) \nNearly 200 years after van Leeuwenhoek got his first glimpse of microbes, the \"Golden Age of Microbiology\" spawned a host of new discoveries between 1857 and 1914. Two famous microbiologists, Louis Pasteur and Robert Koch, were especially active in advancing our understanding of the unseen world of microbes (**[Figure 1.6](#page-30-0)**). Pasteur, a French chemist, showed that individual microbial strains had unique properties and demonstrated that fermentation is caused by microorganisms. He also invented pasteurization, a process used to kill microorganisms responsible for spoilage, and developed vaccines for the treatment of diseases, including rabies, in animals and humans. Koch, a German physician, was the first to demonstrate the connection between a single, isolated microbe and a known human disease. For example, he discovered the bacteria that cause anthrax (*Bacillus anthracis*), cholera (*Vibrio cholera*), and tuberculosis (*Mycobacterium tuberculosis*).[10] We will discuss these famous microbiologists, and others, in later chapters. \n \n \n**Figure 1.6** (a) Louis Pasteur (1822–1895) is credited with numerous innovations that advanced the fields of microbiology and immunology. (b) Robert Koch (1843–1910) identified the specific microbes that cause anthrax, cholera, and tuberculosis. \nAs microbiology has developed, it has allowed the broader discipline of biology to grow and flourish in previously unimagined ways. Much of what we know about human cells comes from our understanding of microbes, and many of the tools we use today to study cells and their genetics derive from work with microbes. \n \n• How did the discovery of microbes change human understanding of disease? \n#### **Micro Connections** \n#### **Microbiology Toolbox** \nBecause individual microbes are generally too small to be seen with the naked eye, the science of microbiology is dependent on technology that can artificially enhance the capacity of our natural senses of perception. Early microbiologists like Pasteur and Koch had fewer tools at their disposal than are found in modern laboratories, making their discoveries and innovations that much more impressive. Later chapters of this text will explore many applications of technology in depth, but for now, here is a brief overview of some of the fundamental tools of the microbiology lab. \n- **Microscopes** produce magnified images of microorganisms, human cells and tissues, and many other types of specimens too small to be observed with the naked eye.\n- **Stains and dyes** are used to add color to microbes so they can be better observed under a microscope. Some dyes can be used on living microbes, whereas others require that the specimens be fixed with chemicals or heat before staining. Some stains only work on certain types of microbes because of differences in their cellular chemical composition.\n- **Growth media** are used to grow microorganisms in a lab setting. Some media are liquids; others are more solid or gel-like. A growth medium provides nutrients, including water, various salts, a source of carbon (like glucose), and a source of nitrogen and amino acids (like yeast extract) so microorganisms can grow and reproduce. Ingredients in a growth medium can be modified to grow unique types of microorganisms.\n- **A Petri dish** is a flat-lidded dish that is typically 10–11 centimeters (cm) in diameter and 1–1.5 cm high. Petri dishes made out of either plastic or glass are used to hold growth media (**[Figure 1.7](#page-32-1)**).\n- **Test tubes** are cylindrical plastic or glass tubes with rounded bottoms and open tops. They can be used to grow microbes in broth, or semisolid or solid growth media.\n- A **Bunsen burner** is a metal apparatus that creates a flame that can be used to sterilize pieces of equipment. A rubber tube carries gas (fuel) to the burner. In many labs, Bunsen burners are being phased out in favor of infrared **microincinerators**, which serve a similar purpose without the safety risks of an open flame.\n- An **inoculation loop** is a handheld tool that ends in a small wire loop (**[Figure 1.7](#page-32-1)**). The loop can be used to streak microorganisms on agar in a Petri dish or to transfer them from one test tube to another. Before each use, the inoculation loop must be sterilized so cultures do not become contaminated. \n \n**Figure 1.7** (a) This Petri dish filled with agar has been streaked with *Legionella*, the bacterium responsible for causing Legionnaire's disease. (b) An inoculation loop like this one can be used to streak bacteria on agar in a Petri dish. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Jeffrey M. Vinocur)",
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"Header 1": "**An Invisible World**",
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"page_content": "#### **Learning Objectives** \n- Describe how microorganisms are classified and distinguished as unique species\n- Compare historical and current systems of taxonomy used to classify microorganisms \nOnce microbes became visible to humans with the help of microscopes, scientists began to realize their enormous diversity. Microorganisms vary in all sorts of ways, including their size, their appearance, and their rates of reproduction. To study this incredibly diverse new array of organisms, researchers needed a way to systematically organize them.\n\n**Taxonomy** is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1701–1778). In 1735, Linnaeus published *Systema Naturae*, an 11-page booklet in which he proposed the Linnaean taxonomy, a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes (**[Figure 1.8](#page-33-0)**). \n \n**Figure 1.8** Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named *Linnaea borealis* in his honor. \nIn his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned). Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus's original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. Species was, and continues to be, the most specific and basic taxonomic unit. \n#### **Evolving Trees of Life (Phylogenies)** \nWith advances in technology, other scientists gradually made refinements to the Linnaean system and eventually created new systems for classifying organisms. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or **phylogenies**, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. In early phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such as the presence or absence of hair or the number of limbs. Now, the analysis is more complicated. Today, phylogenic analyses include genetic, biochemical, and embryological comparisons, as will be discussed later in this chapter. \nLinnaeus's tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (**[Figure 1.9](#page-34-0)**). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria. \n \n**Figure 1.9** Ernst Haeckel's rendering of the tree of life, from his 1866 book *General Morphology of Organisms*, contained three kingdoms: Plantae, Protista, and Animalia. He later added a fourth kingdom, Monera, for unicellular organisms lacking a nucleus. \nNearly 100 years later, in 1969, American ecologist Robert Whittaker (1920–1980) proposed adding another kingdom—Fungi—in his tree of life. Whittaker's tree also contained a level of categorization above the kingdom level—the empire or superkingdom level—to distinguish between organisms that have membrane-bound nuclei in their cells (**eukaryotes**) and those that do not (**prokaryotes**). Empire Prokaryota contained just the Kingdom Monera. The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. Whittaker's fivekingdom tree was considered the standard phylogeny for many years. \n**[Figure 1.10](#page-35-1)** shows how the tree of life has changed over time. Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to determine where they would fit into a tree of life. \n \n**Figure 1.10** This timeline shows how the shape of the tree of life has changed over the centuries. Even today, the taxonomy of living organisms is continually being reevaluated and refined with advances in technology. \n \n• Briefly summarize how our evolving understanding of microorganisms has contributed to changes in the way that organisms are classified. \n#### **Clinical Focus** \n#### **Part 2** \nAntibiotic drugs are specifically designed to kill or inhibit the growth of bacteria. But after a couple of days on antibiotics, Cora shows no signs of improvement. Also, her CSF cultures came back from the lab negative. Since bacteria or fungi were not isolated from Cora's CSF sample, her doctor rules out bacterial and fungal meningitis. Viral meningitis is still a possibility. \nHowever, Cora now reports some troubling new symptoms. She is starting to have difficulty walking. Her muscle stiffness has spread from her neck to the rest of her body, and her limbs sometimes jerk involuntarily. In addition, Cora's cognitive symptoms are worsening. At this point, Cora's doctor becomes very concerned and orders more tests on the CSF samples. \n• What types of microorganisms could be causing Cora's symptoms? \n*Jump to the [next](#page-47-0) Clinical Focus box. Go back to the [previous](#page-26-1) Clinical Focus box.* \n#### **The Role of Genetics in Modern Taxonomy** \nHaeckel's and Whittaker's trees presented hypotheses about the phylogeny of different organisms based on readily observable characteristics. But the advent of molecular genetics in the late 20th century revealed other ways to organize phylogenetic trees. Genetic methods allow for a standardized way to compare all living organisms without relying on observable characteristics that can often be subjective. Modern taxonomy relies heavily on comparing the nucleic acids (deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]) or proteins from different organisms. The more similar the nucleic acids and proteins are between two organisms, the more closely related they are considered to be. \nIn the 1970s, American microbiologist Carl Woese discovered what appeared to be a \"living record\" of the evolution of organisms. He and his collaborator George Fox created a genetics-based tree of life based on similarities and differences they observed in the small subunit ribosomal RNA (rRNA) of different organisms. In the process, they discovered that a certain type of bacteria, called archaebacteria (now known simply as archaea), were significantly different from other bacteria and eukaryotes in terms of the sequence of small subunit rRNA. To accommodate this difference, they created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya (**[Figure 1.11](#page-36-0)**). Genetic analysis of the small subunit rRNA suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. The tree is skewed to show a closer evolutionary relationship between Archaea and Eukarya than they have to Bacteria. \n \n**Figure 1.11** Woese and Fox's phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Eric Gaba) \nScientists continue to use analysis of RNA, DNA, and proteins to determine how organisms are related. One interesting, and complicating, discovery is that of horizontal gene transfer—when a gene of one species is absorbed into another organism's genome. Horizontal gene transfer is especially common in microorganisms and can make it difficult to determine how organisms are evolutionarily related. Consequently, some scientists now think in terms of \"webs of life\" rather than \"trees of life.\" \n \n- In modern taxonomy, how do scientists determine how closely two organisms are related?\n- Explain why the branches on the \"tree of life\" all originate from a single \"trunk.\" \n#### **Naming Microbes** \nIn developing his taxonomy, Linnaeus used a system of **binomial nomenclature**, a two-word naming system for identifying organisms by genus and species. For example, modern humans are in the genus *Homo* and have the species name *sapiens*, so their scientific name in binomial nomenclature is *Homo sapiens*. In binomial nomenclature, the genus part of the name is always capitalized; it is followed by the species name, which is not capitalized. Both names are italicized. \nTaxonomic names in the 18th through 20th centuries were typically derived from Latin, since that was the common language used by scientists when taxonomic systems were first created. Today, newly discovered organisms can be given names derived from Latin, Greek, or English. Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon *Haloquadratum walsbyi* is an example of both of these naming schemes. The genus, *Haloquadratum*, describes the microorganism's saltwater habitat (*halo* is derived from the Greek word for \"salt\") as well as the arrangement of its square cells, which are arranged in square clusters of four cells (*quadratum* is Latin for \"foursquare\"). The species, *walsbyi*, is named after Anthony Edward Walsby, the microbiologist who discovered *Haloquadratum walsbyi* in in 1980. While it might seem easier to give an organism a common descriptive name—like a redheaded woodpecker—we can imagine how that could become problematic. What happens when another species of woodpecker with red head coloring is discovered? The systematic nomenclature scientists use eliminates this potential problem by assigning each organism a single, unique two-word name that is recognized by scientists all over the world. \nIn this text, we will typically abbreviate an organism's genus and species after its first mention. The abbreviated form is simply the first initial of the genus, followed by a period and the full name of the species. For example, the bacterium *Escherichia coli* is shortened to *E. coli* in its abbreviated form. You will encounter this same convention in other scientific texts as well. \n#### **Bergey's Manuals** \nWhether in a tree or a web, microbes can be difficult to identify and classify. Without easily observable macroscopic features like feathers, feet, or fur, scientists must capture, grow, and devise ways to study their biochemical properties to differentiate and classify microbes. Despite these hurdles, a group of microbiologists created and updated a set of manuals for identifying and classifying microorganisms. First published in 1923 and since updated many times, *Bergey's Manual of Determinative Bacteriology* and *Bergey's Manual of Systematic Bacteriology* are the standard references for identifying and classifying different prokaryotes. (**[Appendix D](#page-1244-0)** of this textbook is partly based on Bergey's manuals; it shows how the organisms that appear in this textbook are classified.) Because so many bacteria look identical, methods based on nonvisual characteristics must be used to identify them. For example, biochemical tests can be used to identify chemicals unique to certain species. Likewise, serological tests can be used to identify specific antibodies that will react against the proteins found in certain species. Ultimately, DNA and rRNA sequencing can be used both for identifying a particular bacterial species and for classifying newly discovered species. \n \n• What is binomial nomenclature and why is it a useful tool for naming organisms? \n• Explain why a resource like one of Bergey's manuals would be helpful in identifying a microorganism in a sample. \n#### **Micro Connections** \n#### **Same Name, Different Strain** \nWithin one species of microorganism, there can be several subtypes called strains. While different strains may be nearly identical genetically, they can have very different attributes. The bacterium *Escherichia coli* is infamous for causing food poisoning and traveler's diarrhea. However, there are actually many different strains of *E. coli*, and they vary in their ability to cause disease. \nOne pathogenic (disease-causing) *E. coli* strain that you may have heard of is *E. coli* O157:H7. In humans, infection from *E. coli* O157:H7 can cause abdominal cramps and diarrhea. Infection usually originates from contaminated water or food, particularly raw vegetables and undercooked meat. In the 1990s, there were several large outbreaks of *E. coli* O157:H7 thought to have originated in undercooked hamburgers. \nWhile *E. coli* O157:H7 and some other strains have given *E. coli* a bad name, most *E. coli* strains do not cause disease. In fact, some can be helpful. Different strains of *E. coli* found naturally in our gut help us digest our food, provide us with some needed chemicals, and fight against pathogenic microbes. \n#### **Link to Learning** \n \nLearn more about phylogenetic trees by exploring the Wellcome Trust's interactive Tree of Life. The **[website \\(https://www.openstax.org/l/22wellcome\\)](https://www.openstax.org/l/22wellcome)** contains information, photos, and animations about many different organisms. Select two organisms to see how they are evolutionarily related.\n\n#### **Learning Objectives** \n- List the various types of microorganisms and describe their defining characteristics\n- Give examples of different types of cellular and viral microorganisms and infectious agents\n- Describe the similarities and differences between archaea and bacteria\n- Provide an overview of the field of microbiology \nMost microbes are unicellular and small enough that they require artificial magnification to be seen. However, there are some unicellular microbes that are visible to the naked eye, and some multicellular organisms that are microscopic. An object must measure about 100 micrometers (µm) to be visible without a microscope, but most microorganisms are many times smaller than that. For some perspective, consider that a typical animal cell measures roughly 10 µm across but is still microscopic. Bacterial cells are typically about 1 µm, and viruses can be 10 times smaller than bacteria (**[Figure 1.12](#page-39-0)**). See **[Table 1.1](#page-39-1)** for units of length used in microbiology. \n \n**Figure 1.12** The relative sizes of various microscopic and nonmicroscopic objects. Note that a typical virus measures about 100 nm, 10 times smaller than a typical bacterium (~1 µm), which is at least 10 times smaller than a typical plant or animal cell (~10–100 µm). An object must measure about 100 µm to be visible without a microscope. \n| Metric Unit | Meaning of Prefix | Metric Equivalent |\n|-----------------|-------------------|-------------------------------|\n| meter (m) | — | 1 m = 100 m |\n| decimeter (dm) | 1/10 | 1 dm = 0.1 m = 10−1 m |\n| centimeter (cm) | 1/100 | 1 cm = 0.01 m = 10−2 m |\n| millimeter (mm) | 1/1000 | 1 mm = 0.001 m = 10−3 m |\n| micrometer (μm) | 1/1,000,000 | 1 μm = 0.000001 m = 10−6 m |\n| nanometer (nm) | 1/1,000,000,000 | 1 nm = 0.000000001 m = 10−9 m | \n**Units of Length Commonly Used in Microbiology** \n**Table 1.1** \nMicroorganisms differ from each other not only in size, but also in structure, habitat, metabolism, and many other characteristics. While we typically think of microorganisms as being unicellular, there are also many multicellular organisms that are too small to be seen without a microscope. Some microbes, such as viruses, are even **acellular** (not composed of cells). \nMicroorganisms are found in each of the three domains of life: Archaea, Bacteria, and Eukarya. Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus), whereas microbes in the domain Eukarya are eukaryotes (their cells have a nucleus). Some microorganisms, such as viruses, do not fall within any of the three domains of life. In this section, we will briefly introduce each of the broad groups of microbes. Later chapters will go into greater depth about the diverse species within each group. \n#### **Link to Learning** \n \nHow big is a bacterium or a virus compared to other objects? Check out this **[interactive website \\(https://www.openstax.org/l/22relsizes\\)](https://www.openstax.org/l/22relsizes)** to get a feel for the scale of different microorganisms.\n\n**Bacteria** are found in nearly every habitat on earth, including within and on humans. Most bacteria are harmless or helpful, but some are **pathogens**, causing disease in humans and other animals. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. Most bacteria have cell walls that contain peptidoglycan. \nBacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio). **[Figure 1.13](#page-40-0)** shows examples of these shapes. \n \n**Figure 1.13** Common bacterial shapes. Note how coccobacillus is a combination of spherical (coccus) and rodshaped (bacillus). (credit \"Coccus\": modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit \"Coccobacillus\": modification of work by Janice Carr, Centers for Disease Control and Prevention; credit \"Spirochete\": Centers for Disease Control and Prevention) \nThey have a wide range of metabolic capabilities and can grow in a variety of environments, using different combinations of nutrients. Some bacteria are photosynthetic, such as oxygenic cyanobacteria and anoxygenic green sulfur and green nonsulfur bacteria; these bacteria use energy derived from sunlight, and fix carbon dioxide for growth. Other types of bacteria are nonphotosynthetic, obtaining their energy from organic or inorganic compounds in their environment. \n**Archaea** are also unicellular prokaryotic organisms. Archaea and bacteria have different evolutionary histories, as well as significant differences in genetics, metabolic pathways, and the composition of their cell walls and membranes. Unlike most bacteria, archaeal cell walls do not contain peptidoglycan, but their cell walls are often composed of a similar substance called pseudopeptidoglycan. Like bacteria, archaea are found in nearly every habitat on earth, even extreme environments that are very cold, very hot, very basic, or very acidic (**[Figure 1.14](#page-41-0)**). Some archaea live in the human body, but none have been shown to be human pathogens. \n \n**Figure 1.14** Some archaea live in extreme environments, such as the Morning Glory pool, a hot spring in Yellowstone National Park. The color differences in the pool result from the different communities of microbes that are able to thrive at various water temperatures. \n \n- What are the two main types of prokaryotic organisms?\n- Name some of the defining characteristics of each type.\n\nThe domain Eukarya contains all eukaryotes, including uni- or multicellular eukaryotes such as protists, fungi, plants, and animals. The major defining characteristic of eukaryotes is that their cells contain a nucleus. \n#### **Protists** \n**Protists** are unicellular eukaryotes that are not plants, animals, or fungi. Algae and protozoa are examples of protists. \n**Algae** (singular: alga) are plant-like protists that can be either unicellular or multicellular (**[Figure 1.15](#page-42-0)**). Their cells are surrounded by cell walls made of cellulose, a type of carbohydrate. Algae are photosynthetic organisms that extract energy from the sun and release oxygen and carbohydrates into their environment. Because other organisms can use their waste products for energy, algae are important parts of many ecosystems. Many consumer products contain ingredients derived from algae, such as carrageenan or alginic acid, which are found in some brands of ice cream, salad dressing, beverages, lipstick, and toothpaste. A derivative of algae also plays a prominent role in the microbiology laboratory. Agar, a gel derived from algae, can be mixed with various nutrients and used to grow microorganisms in a Petri dish. Algae are also being developed as a possible source for biofuels. \n \n**Figure 1.15** Assorted diatoms, a kind of algae, live in annual sea ice in McMurdo Sound, Antarctica. Diatoms range in size from 2 μm to 200 μm and are visualized here using light microscopy. (credit: modification of work by National Oceanic and Atmospheric Administration) \n**Protozoa** (singular: protozoan) are protists that make up the backbone of many food webs by providing nutrients for other organisms. Protozoa are very diverse. Some protozoa move with help from hair-like structures called cilia or whip-like structures called flagella. Others extend part of their cell membrane and cytoplasm to propel themselves forward. These cytoplasmic extensions are called pseudopods (\"false feet\"). Some protozoa are photosynthetic; others feed on organic material. Some are free-living, whereas others are parasitic, only able to survive by extracting nutrients from a host organism. Most protozoa are harmless, but some are pathogens that can cause disease in animals or humans (**[Figure 1.16](#page-42-1)**). \n \n**Figure 1.16** *Giardia lamblia*, an intestinal protozoan parasite that infects humans and other mammals, causing severe diarrhea. (credit: modification of work by Centers for Disease Control and Prevention) \n#### **Fungi** \n**Fungi** (singular: fungus) are also eukaryotes. Some multicellular fungi, such as mushrooms, resemble plants, but they are actually quite different. Fungi are not photosynthetic, and their cell walls are usually made out of chitin rather than cellulose. \nUnicellular fungi—yeasts—are included within the study of microbiology. There are more than 1000 known species. Yeasts are found in many different environments, from the deep sea to the human navel. Some yeasts have beneficial \nuses, such as causing bread to rise and beverages to ferment; but yeasts can also cause food to spoil. Some even cause diseases, such as vaginal yeast infections and oral thrush (**[Figure 1.17](#page-43-0)**). \n \n**Figure 1.17** *Candida albicans* is a unicellular fungus, or yeast. It is the causative agent of vaginal yeast infections as well as oral thrush, a yeast infection of the mouth that commonly afflicts infants. *C. albicans* has a morphology similar to that of coccus bacteria; however, yeast is a eukaryotic organism (note the nuclei) and is much larger. (credit: modification of work by Centers for Disease Control and Prevention) \nOther fungi of interest to microbiologists are multicellular organisms called **molds**. Molds are made up of long filaments that form visible colonies (**[Figure 1.18](#page-43-1)**). Molds are found in many different environments, from soil to rotting food to dank bathroom corners. Molds play a critical role in the decomposition of dead plants and animals. Some molds can cause allergies, and others produce disease-causing metabolites called mycotoxins. Molds have been used to make pharmaceuticals, including penicillin, which is one of the most commonly prescribed antibiotics, and cyclosporine, used to prevent organ rejection following a transplant. \n \n**Figure 1.18** Large colonies of microscopic fungi can often be observed with the naked eye, as seen on the surface of these moldy oranges. \n \n• Name two types of protists and two types of fungi. \n• Name some of the defining characteristics of each type.\n\nMulticellular parasitic worms called **helminths** are not technically microorganisms, as most are large enough to see without a microscope. However, these worms fall within the field of microbiology because diseases caused by helminths involve microscopic eggs and larvae. One example of a helminth is the guinea worm, or *Dracunculus medinensis*, which causes dizziness, vomiting, diarrhea, and painful ulcers on the legs and feet when the worm works its way out of the skin (**[Figure 1.19](#page-44-0)**). Infection typically occurs after a person drinks water containing water fleas infected by guinea-worm larvae. In the mid-1980s, there were an estimated 3.5 million cases of guinea-worm disease, but the disease has been largely eradicated. In 2014, there were only 126 cases reported, thanks to the coordinated efforts of the World Health Organization (WHO) and other groups committed to improvements in drinking water sanitation.[11][12] \n \n \n**Figure 1.19** (a) The beef tapeworm, *Taenia saginata*, infects both cattle and humans. *T. saginata* eggs are microscopic (around 50 µm), but adult worms like the one shown here can reach 4–10 m, taking up residence in the digestive system. (b) An adult guinea worm, *Dracunculus medinensis*, is removed through a lesion in the patient's skin by winding it around a matchstick. (credit a, b: modification of work by Centers for Disease Control and Prevention) \n#### **Viruses** \n**Viruses** are **acellular** microorganisms, which means they are not composed of cells. Essentially, a virus consists of proteins and genetic material—either DNA or RNA, but never both—that are inert outside of a host organism. However, by incorporating themselves into a host cell, viruses are able to co-opt the host's cellular mechanisms to multiply and infect other hosts. \nViruses can infect all types of cells, from human cells to the cells of other microorganisms. In humans, viruses are responsible for numerous diseases, from the common cold to deadly Ebola (**[Figure 1.20](#page-45-0)**). However, many viruses do not cause disease. \n11. C. Greenaway \"Dracunculiasis (Guinea Worm Disease).\" *Canadian Medical Association Journal* 170 no. 4 (2004):495–500. \n12. World Health Organization. \"Dracunculiasis (Guinea-Worm Disease).\" *WHO*. 2015. http://www.who.int/mediacentre/factsheets/fs359/ en/. Accessed October 2, 2015. \n \n**Figure 1.20** (a) Members of the Coronavirus family can cause respiratory infections like the common cold, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Here they are viewed under a transmission electron microscope (TEM). (b) Ebolavirus, a member of the Filovirus family, as visualized using a TEM. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Thomas W. Geisbert) \n \n- Are helminths microorganisms? Explain why or why not.\n- How are viruses different from other microorganisms?\n\n**Microbiology** is a broad term that encompasses the study of all different types of microorganisms. But in practice, microbiologists tend to specialize in one of several subfields. For example, **bacteriology** is the study of bacteria; **mycology** is the study of fungi; **protozoology** is the study of protozoa; **parasitology** is the study of helminths and other parasites; and **virology** is the study of viruses (**[Figure 1.21](#page-46-0)**). **Immunology**, the study of the immune system, is often included in the study of microbiology because host–pathogen interactions are central to our understanding of infectious disease processes. Microbiologists can also specialize in certain areas of microbiology, such as clinical microbiology, environmental microbiology, applied microbiology, or food microbiology. \nIn this textbook, we are primarily concerned with clinical applications of microbiology, but since the various subfields of microbiology are highly interrelated, we will often discuss applications that are not strictly clinical. \n \n**Figure 1.21** A virologist samples eggs from this nest to be tested for the influenza A virus, which causes avian flu in birds. (credit: U.S. Fish and Wildlife Service) \n#### **Eye on Ethics** \n \n#### **Bioethics in Microbiology** \nIn the 1940s, the U.S. government was looking for a solution to a medical problem: the prevalence of sexually transmitted diseases (STDs) among soldiers. Several now-infamous government-funded studies used human subjects to research common STDs and treatments. In one such study, American researchers intentionally exposed more than 1300 human subjects in Guatemala to syphilis, gonorrhea, and chancroid to determine the ability of penicillin and other antibiotics to combat these diseases. Subjects of the study included Guatemalan soldiers, prisoners, prostitutes, and psychiatric patients—none of whom were informed that they were taking part in the study. Researchers exposed subjects to STDs by various methods, from facilitating intercourse with infected prostitutes to inoculating subjects with the bacteria known to cause the diseases. This latter method involved making a small wound on the subject's genitals or elsewhere on the body, and then putting bacteria directly into the wound.[13] In 2011, a U.S. government commission tasked with investigating the experiment revealed that only some of the subjects were treated with penicillin, and 83 subjects died by 1953, likely as a result of the study.[14] \nUnfortunately, this is one of many horrific examples of microbiology experiments that have violated basic ethical standards. Even if this study had led to a life-saving medical breakthrough (it did not), few would argue that its methods were ethically sound or morally justifiable. But not every case is so clear cut. Professionals working in clinical settings are frequently confronted with ethical dilemmas, such as working with patients who decline a vaccine or life-saving blood transfusion. These are just two examples of life-and-death decisions that \nmay intersect with the religious and philosophical beliefs of both the patient and the health-care professional. \nNo matter how noble the goal, microbiology studies and clinical practice must be guided by a certain set of ethical principles. Studies must be done with integrity. Patients and research subjects provide informed consent (not only agreeing to be treated or studied but demonstrating an understanding of the purpose of the study and any risks involved). Patients' rights must be respected. Procedures must be approved by an institutional review board. When working with patients, accurate record-keeping, honest communication, and confidentiality are paramount. Animals used for research must be treated humanely, and all protocols must be approved by an institutional animal care and use committee. These are just a few of the ethical principles explored in the *Eye on Ethics* boxes throughout this book. \n#### **Clinical Focus** \n#### **Resolution** \nCora's CSF samples show no signs of inflammation or infection, as would be expected with a viral infection. However, there is a high concentration of a particular protein, 14-3-3 protein, in her CSF. An electroencephalogram (EEG) of her brain function is also abnormal. The EEG resembles that of a patient with a neurodegenerative disease like Alzheimer's or Huntington's, but Cora's rapid cognitive decline is not consistent with either of these. Instead, her doctor concludes that Cora has Creutzfeldt-Jakob disease (CJD), a type of transmissible spongiform encephalopathy (TSE). \nCJD is an extremely rare disease, with only about 300 cases in the United States each year. It is not caused by a bacterium, fungus, or virus, but rather by prions—which do not fit neatly into any particular category of microbe. Like viruses, prions are not found on the tree of life because they are acellular. Prions are extremely small, about one-tenth the size of a typical virus. They contain no genetic material and are composed solely of a type of abnormal protein. \nCJD can have several different causes. It can be acquired through exposure to the brain or nervoussystem tissue of an infected person or animal. Consuming meat from an infected animal is one way such exposure can occur. There have also been rare cases of exposure to CJD through contact with contaminated surgical equipment[15] and from cornea and growth-hormone donors who unknowingly had CJD.[16][17] In rare cases, the disease results from a specific genetic mutation that can sometimes be hereditary. However, in approximately 85% of patients with CJD, the cause of the disease is spontaneous (or sporadic) and has no identifiable cause.[18] Based on her symptoms and their rapid progression, Cora is diagnosed with sporadic CJD. \nUnfortunately for Cora, CJD is a fatal disease for which there is no approved treatment. Approximately 90% of patients die within 1 year of diagnosis.[19] Her doctors focus on limiting her pain and cognitive symptoms as her disease progresses. Eight months later, Cora dies. Her CJD diagnosis is confirmed with a brain autopsy. \n*Go back to the [previous](#page-35-0) Clinical Focus box.* \n- 13. Kara Rogers. \"Guatemala Syphilis Experiment: American Medical Research Project\". *Encylopaedia Britannica*. http://www.britannica.com/event/Guatemala-syphilis-experiment. Accessed June 24, 2015.\n- 14. Susan Donaldson James. \"Syphilis Experiments Shock, But So Do Third-World Drug Trials.\" *ABC World News*. August 30, 2011. http://abcnews.go.com/Health/guatemala-syphilis-experiments-shock-us-drug-trials-exploit/story?id=14414902. Accessed June 24, 2015.\n- 15. Greg Botelho. \"Case of Creutzfeldt-Jakob Disease Confirmed in New Hampshire.\" *CNN*. 2013. http://www.cnn.com/2013/09/20/health/ creutzfeldt-jakob-brain-disease/.\n- 16. P. Rudge et al. \"Iatrogenic CJD Due to Pituitary-Derived Growth Hormone With Genetically Determined Incubation Times of Up to 40 Years.\" *Brain* 138 no. 11 (2015): 3386–3399.\n- 17. J.G. Heckmann et al. \"Transmission of Creutzfeldt-Jakob Disease via a Corneal Transplant.\" *Journal of Neurology, Neurosurgery & Psychiatry* 63 no. 3 (1997): 388–390.",
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"page_content": "#### **[1.1 What Our Ancestors Knew](#page-25-0)** \n• **Microorganisms** (or **microbes**) are living organisms that are generally too small to be seen without a microscope. \n- Throughout history, humans have used microbes to make fermented foods such as beer, bread, cheese, and wine.\n- Long before the invention of the microscope, some people theorized that infection and disease were spread by living things that were too small to be seen. They also correctly intuited certain principles regarding the spread of disease and immunity.\n- Antonie van Leeuwenhoek, using a microscope, was the first to actually describe observations of bacteria, in 1675.\n- During the Golden Age of Microbiology (1857–1914), microbiologists, including Louis Pasteur and Robert Koch, discovered many new connections between the fields of microbiology and medicine. \n#### **[1.2 A Systematic Approach](#page-32-0)** \n- Carolus Linnaeus developed a taxonomic system for categorizing organisms into related groups.\n- **Binomial nomenclature** assigns organisms Latinized scientific names with a genus and species designation.\n- A **phylogenetic tree** is a way of showing how different organisms are thought to be related to one another from an evolutionary standpoint.\n- The first phylogenetic tree contained kingdoms for plants and animals; Ernst Haeckel proposed adding kingdom for protists.\n- Robert Whittaker's tree contained five kingdoms: Animalia, Plantae, Protista, Fungi, and Monera.\n- Carl Woese used small subunit ribosomal RNA to create a phylogenetic tree that groups organisms into three domains based on their genetic similarity.\n- Bergey's manuals of determinative and systemic bacteriology are the standard references for identifying and classifying bacteria, respectively.\n- Bacteria can be identified through biochemical tests, DNA/RNA analysis, and serological testing methods. \n#### **[1.3 Types of Microorganisms](#page-38-0)** \n- Microorganisms are very diverse and are found in all three domains of life: Archaea, Bacteria, and Eukarya.\n- **Archaea** and **bacteria** are classified as prokaryotes because they lack a cellular nucleus. Archaea differ from bacteria in evolutionary history, genetics, metabolic pathways, and cell wall and membrane composition.\n- Archaea inhabit nearly every environment on earth, but no archaea have been identified as human pathogens.\n- **Eukaryotes** studied in microbiology include algae, protozoa, fungi, and helminths.\n- **Algae** are plant-like organisms that can be either unicellular or multicellular, and derive energy via photosynthesis.\n- **Protozoa** are unicellular organisms with complex cell structures; most are motile.\n- Microscopic **fungi** include **molds** and **yeasts**.\n- **Helminths** are multicellular parasitic worms. They are included in the field of microbiology because their eggs and larvae are often microscopic.\n- **Viruses** are acellular microorganisms that require a host to reproduce.\n- The field of microbiology is extremely broad. Microbiologists typically specialize in one of many subfields, but all health professionals need a solid foundation in clinical microbiology. \n18. National Institute of Neurological Disorders and Stroke. \"Creutzfeldt-Jakob Disease Fact Sheet.\" *NIH*. 2015. http://www.ninds.nih.gov/ disorders/cjd/detail\\_cjd.htm#288133058. \n19. National Institute of Neurological Disorders and Stroke. \"Creutzfeldt-Jakob Disease Fact Sheet.\" *NIH*. 2015. http://www.ninds.nih.gov/ disorders/cjd/detail\\_cjd.htm#288133058. Accessed June 22, 2015.\n\n#### **Multiple Choice** \n- **1.** Which of the following foods is NOT made by fermentation?\n- a. beer\n- b. bread\n- c. cheese\n- d. orange juice\n- **2.** Who is considered the \"father of Western medicine\"?\n- a. Marcus Terentius Varro\n- b. Thucydides\n- c. Antonie van Leeuwenhoek\n- d. Hippocrates\n- **3.** Who was the first to observe \"animalcules\" under the microscope?\n- a. Antonie van Leeuwenhoek\n- b. Ötzi the Iceman\n- c. Marcus Terentius Varro\n- d. Robert Koch\n- **4.** Who proposed that swamps might harbor tiny, disease-causing animals too small to see?\n- a. Thucydides\n- b. Marcus Terentius Varro\n- c. Hippocrates\n- d. Louis Pasteur\n- **5.** Which of the following was NOT a kingdom in Linnaeus's taxonomy?\n- a. animal\n- b. mineral\n- c. protist\n- d. plant\n- **6.** Which of the following is a correct usage of binomial nomenclature?\n- a. Homo Sapiens\n- b. *homo sapiens*\n- c. *Homo sapiens*\n- d. *Homo Sapiens*\n- **7.** Which scientist proposed adding a kingdom for protists?\n- a. Carolus Linnaeus\n- b. Carl Woese\n- c. Robert Whittaker\n- d. Ernst Haeckel \n- **8.** Which of the following is NOT a domain in Woese and Fox's phylogenetic tree?\n- a. Plantae\n- b. Bacteria\n- c. Archaea\n- d. Eukarya\n- **9.** Which of the following is the standard resource for identifying bacteria?\n- a. *Systema Naturae*\n- b. Bergey's *Manual of Determinative Bacteriology*\n- c. Woese and Fox's phylogenetic tree\n- d. Haeckel's *General Morphology of Organisms*\n- **10.** Which of the following types of microorganisms is photosynthetic?\n- a. yeast\n- b. virus\n- c. helminth\n- d. alga\n- **11.** Which of the following is a prokaryotic microorganism?\n- a. helminth\n- b. protozoan\n- c. cyanobacterium\n- d. mold\n- **12.** Which of the following is acellular?\n- a. virus\n- b. bacterium\n- c. fungus\n- d. protozoan\n- **13.** Which of the following is a type of fungal microorganism?\n- a. bacterium\n- b. protozoan\n- c. alga\n- d. yeast\n- **14.** Which of the following is not a subfield of microbiology?\n- a. bacteriology\n- b. botany\n- c. clinical microbiology\n- d. virology \n| | Fill in the Blank |\n|-----|--------------------------------------------------------------------------------------------------------|\n| 15. | Thucydides is known as the father of |\n| 16. | Researchers think that Ötzi the Iceman may have been infected with disease. |\n| 17. | The process by which microbes turn grape juice into wine is called |\n| 18. | In binomial nomenclature, an organism's scientific name includes its and |\n| 19. | Whittaker proposed adding the kingdoms and to his phylogenetic tree. |\n| 20. | are organisms without membrane-bound nuclei. |\n| 21. | are microorganisms that are not included in phylogenetic trees because they are acellular. |\n| 22. | A is a disease-causing microorganism. |\n| 23. | Multicellular parasitic worms studied by microbiologists are called |\n| 24. | The study of viruses is |\n| 25. | The cells of prokaryotic organisms lack a |\n| | Short Answer |\n| 26. | What did Thucydides learn by observing the Athenian plague? |\n| 27. | Why was the invention of the microscope important for microbiology? |\n| 28. | What are some ways people use microbes? |\n| 29. | What is a phylogenetic tree? |\n| 30. | Which of the five kingdoms in Whittaker's phylogenetic tree are prokaryotic, and which are eukaryotic? |\n| 31. | What molecule did Woese and Fox use to construct their phylogenetic tree? |\n| 32. | Name some techniques that can be used to identify and differentiate species of bacteria. |\n| 33. | Describe the differences between bacteria and archaea. |\n| | | \n- **34.** Name three structures that various protozoa use for locomotion.\n- **35.** Describe the actual and relative sizes of a virus, a bacterium, and a plant or animal cell. \n#### **Critical Thinking** \n- **36.** Explain how the discovery of fermented foods likely benefited our ancestors.\n- **37.** What evidence would you use to support this statement: Ancient people thought that disease was transmitted by things they could not see.\n- **38.** Why is using binomial nomenclature more useful than using common names?",
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"page_content": "#### **Learning Objectives** \n- Identify and define the characteristics of electromagnetic radiation (EMR) used in microscopy\n- Explain how lenses are used in microscopy to manipulate visible and ultraviolet (UV) light \nVisible light consists of electromagnetic waves that behave like other waves. Hence, many of the properties of light that are relevant to microscopy can be understood in terms of light's behavior as a wave. An important property of light waves is the **wavelength**, or the distance between one peak of a wave and the next peak. The height of each peak (or depth of each trough) is called the **amplitude**. In contrast, the **frequency** of the wave is the rate of vibration of the wave, or the number of wavelengths within a specified time period (**[Figure 2.2](#page-53-1)**). \n \n**Figure 2.2** (a) The amplitude is the height of a wave, whereas the wavelength is the distance between one peak and the next. (b) These waves have different frequencies, or rates of vibration. The wave at the top has the lowest frequency, since it has the fewest peaks per unit time. The wave at the bottom has the highest frequency.\n\nLight waves interact with materials by being reflected, absorbed, or transmitted. **Reflection** occurs when a wave bounces off of a material. For example, a red piece of cloth may reflect red light to our eyes while absorbing other colors of light. **Absorbance** occurs when a material captures the energy of a light wave. In the case of glow-in-thedark plastics, the energy from light can be absorbed and then later re-emitted as another form of phosphorescence. Transmission occurs when a wave travels through a material, like light through glass (the process of transmission is called **transmittance**). When a material allows a large proportion of light to be transmitted, it may do so because it is thinner, or more transparent (having more **transparency** and less **opacity**). **[Figure 2.3](#page-54-0)** illustrates the difference \n#### **Clinical Focus** \n#### **Part 1** \nCindy, a 17-year-old counselor at a summer sports camp, scraped her knee playing basketball 2 weeks ago. At the time, she thought it was only a minor abrasion that would heal, like many others before it. Instead, the wound began to look like an insect bite and has continued to become increasingly painful and swollen. \nThe camp nurse examines the lesion and observes a large amount of pus oozing from the surface. Concerned that Cindy may have developed a potentially aggressive infection, she swabs the wound to collect a sample from the infection site. Then she cleans out the pus and dresses the wound, instructing Cindy to keep the area clean and to come back the next day. When Cindy leaves, the nurse sends the sample to the closest medical lab to be analyzed under a microscope. \n• What are some things we can learn about these bacteria by looking at them under a microscope? \n*Jump to the [next](#page-67-0) Clinical Focus box.* \nbetween transparency and opacity. \n \n \n**Figure 2.3** (a) A Petri dish is made of transparent plastic or glass, which allows transmission of a high proportion of light. This transparency allows us to see through the sides of the dish to view the contents. (b) This slice of an iron meteorite is opaque (i.e., it has opacity). Light is not transmitted through the material, making it impossible to see the part of the hand covered by the object. (credit a: modification of work by Umberto Salvagnin; credit b: modification of work by \"Waifer X\"/Flickr) \nLight waves can also interact with each other by **interference**, creating complex patterns of motion. Dropping two pebbles into a puddle causes the waves on the puddle's surface to interact, creating complex interference patterns. Light waves can interact in the same way. \nIn addition to interfering with each other, light waves can also interact with small objects or openings by bending or scattering. This is called **diffraction**. Diffraction is larger when the object is smaller relative to the wavelength of the light (the distance between two consecutive peaks of a light wave). Often, when waves diffract in different directions around an obstacle or opening, they will interfere with each other. \n \n- If a light wave has a long wavelength, is it likely to have a low or high frequency?\n- If an object is transparent, does it reflect, absorb, or transmit light? \n#### **Lenses and Refraction** \nIn the context of microscopy, **refraction** is perhaps the most important behavior exhibited by light waves. Refraction occurs when light waves change direction as they enter a new medium (**[Figure 2.4](#page-55-0)**). Different transparent materials transmit light at different speeds; thus, light can change speed when passing from one material to another. This change in speed usually also causes a change in direction (refraction), with the degree of change dependent on the angle of the incoming light. \n \n**Figure 2.4** (a) Refraction occurs when light passes from one medium, such as air, to another, such as glass, changing the direction of the light rays. (b) As shown in this diagram, light rays passing from one medium to another may be either refracted or reflected. \nThe extent to which a material slows transmission speed relative to empty space is called the **refractive index** of that material. Large differences between the refractive indices of two materials will result in a large amount of refraction when light passes from one material to the other. For example, light moves much more slowly through water than through air, so light entering water from air can change direction greatly. We say that the water has a higher refractive index than air (**[Figure 2.5](#page-55-1)**). \n \n**Figure 2.5** This straight pole appears to bend at an angle as it enters the water. This optical illusion is due to the large difference between the refractive indices of air and water. \nWhen light crosses a boundary into a material with a higher refractive index, its direction turns to be closer to perpendicular to the boundary (i.e., more toward a normal to that boundary; see **[Figure 2.5](#page-55-1)**). This is the principle behind lenses. We can think of a lens as an object with a curved boundary (or a collection of prisms) that collects all of the light that strikes it and refracts it so that it all meets at a single point called the **image point (focus)**. A convex lens can be used to magnify because it can focus at closer range than the human eye, producing a larger image. Concave lenses and mirrors can also be used in microscopes to redirect the light path. **[Figure 2.6](#page-56-0)** shows the **focal point** (the image point when light entering the lens is parallel) and the **focal length** (the distance to the focal point) for convex and concave lenses. \n \n**Figure 2.6** (a) A lens is like a collection of prisms, such as the one shown here. (b) When light passes through a convex lens, it is refracted toward a focal point on the other side of the lens. The focal length is the distance to the focal point. (c) Light passing through a concave lens is refracted away from a focal point in front of the lens. \nThe human eye contains a lens that enables us to see images. This lens focuses the light reflecting off of objects in front of the eye onto the surface of the retina, which is like a screen in the back of the eye. Artificial lenses placed in front of the eye (contact lenses, glasses, or microscopic lenses) focus light before it is focused (again) by the lens of the eye, manipulating the image that ends up on the retina (e.g., by making it appear larger). \nImages are commonly manipulated by controlling the distances between the object, the lens, and the screen, as well as the curvature of the lens. For example, for a given amount of curvature, when an object is closer to the lens, the focal points are farther from the lens. As a result, it is often necessary to manipulate these distances to create a focused image on a screen. Similarly, more curvature creates image points closer to the lens and a larger image when the image is in focus. This property is often described in terms of the focal distance, or distance to the focal point. \n \n- Explain how a lens focuses light at the image point.\n- Name some factors that affect the focal length of a lens.\n\nVisible light is just one form of electromagnetic radiation (EMR), a type of energy that is all around us. Other forms of EMR include microwaves, X-rays, and radio waves, among others. The different types of EMR fall on the electromagnetic spectrum, which is defined in terms of wavelength and frequency. The spectrum of visible light occupies a relatively small range of frequencies between infrared and ultraviolet light (**[Figure 2.7](#page-57-0)**). \n \n**Figure 2.7** The electromagnetic spectrum ranges from high-frequency gamma rays to low-frequency radio waves. Visible light is the relatively small range of electromagnetic frequencies that can be sensed by the human eye. On the electromagnetic spectrum, visible light falls between ultraviolet and infrared light. (credit: modification of work by Johannes Ahlmann) \nWhereas wavelength represents the distance between adjacent peaks of a light wave, frequency, in a simplified definition, represents the rate of oscillation. Waves with higher frequencies have shorter wavelengths and, therefore, have more oscillations per unit time than lower-frequency waves. Higher-frequency waves also contain more energy than lower-frequency waves. This energy is delivered as elementary particles called photons. Higher-frequency waves deliver more energetic photons than lower-frequency waves. \nPhotons with different energies interact differently with the retina. In the spectrum of visible light, each color corresponds to a particular frequency and wavelength (**[Figure 2.7](#page-57-0)**).The lowest frequency of visible light appears as the color red, whereas the highest appears as the color violet. When the retina receives visible light of many different frequencies, we perceive this as white light. However, white light can be separated into its component colors using refraction. If we pass white light through a prism, different colors will be refracted in different directions, creating a rainbow-like spectrum on a screen behind the prism. This separation of colors is called **dispersion**, and it occurs because, for a given material, the refractive index is different for different frequencies of light. \nCertain materials can refract nonvisible forms of EMR and, in effect, transform them into visible light. Certain **fluorescent** dyes, for instance, absorb ultraviolet or blue light and then use the energy to emit photons of a different color, giving off light rather than simply vibrating. This occurs because the energy absorption causes electrons to jump to higher energy states, after which they then almost immediately fall back down to their ground states, emitting specific amounts of energy as photons. Not all of the energy is emitted in a given photon, so the emitted photons will be of lower energy and, thus, of lower frequency than the absorbed ones. Thus, a dye such as Texas red may be excited by blue light, but emit red light; or a dye such as fluorescein isothiocyanate (FITC) may absorb (invisible) highenergy ultraviolet light and emit green light (**[Figure 2.8](#page-58-0)**). In some materials, the photons may be emitted following a delay after absorption; in this case, the process is called **phosphorescence**. Glow-in-the-dark plastic works by using phosphorescent material. \n \n**Figure 2.8** The fluorescent dyes absorbed by these bovine pulmonary artery endothelial cells emit brilliant colors when excited by ultraviolet light under a fluorescence microscope. Various cell structures absorb different dyes. The nuclei are stained blue with 4',6-diamidino-2-phenylindole (DAPI); microtubles are marked green by an antibody bound to FITC; and actin filaments are labeled red with phalloidin bound to tetramethylrhodamine (TRITC). (credit: National Institutes of Health) \n \n- Which has a higher frequency: red light or green light?\n- Explain why dispersion occurs when white light passes through a prism.\n- Why do fluorescent dyes emit a different color of light than they absorb?\n\nMicroscopes magnify images and use the properties of light to create useful images of small objects. **Magnification** is defined as the ability of a lens to enlarge the image of an object when compared to the real object. For example, a magnification of 10⨯ means that the image appears 10 times the size of the object as viewed with the naked eye. \nGreater magnification typically improves our ability to see details of small objects, but magnification alone is not sufficient to make the most useful images. It is often useful to enhance the **resolution** of objects: the ability to tell that two separate points or objects are separate. A low-resolution image appears fuzzy, whereas a high-resolution image appears sharp. Two factors affect resolution. The first is wavelength. Shorter wavelengths are able to resolve smaller objects; thus, an electron microscope has a much higher resolution than a light microscope, since it uses an electron beam with a very short wavelength, as opposed to the long-wavelength visible light used by a light microscope. The second factor that affects resolution is **numerical aperture**, which is a measure of a lens's ability to gather light. The higher the numerical aperture, the better the resolution.",
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"page_content": "#### **Learning Objectives** \n- Describe historical developments and individual contributions that led to the invention and development of the microscope\n- Compare and contrast the features of simple and compound microscopes \nSome of the fundamental characteristics and functions of microscopes can be understood in the context of the history of their use. Italian scholar Girolamo Fracastoro is regarded as the first person to formally postulate that disease was spread by tiny invisible *seminaria*, or \"seeds of the contagion.\" In his book *De Contagione* (1546), he proposed that these seeds could attach themselves to certain objects (which he called *fomes* [cloth]) that supported their transfer from person to person. However, since the technology for seeing such tiny objects did not yet exist, the existence of the *seminaria* remained hypothetical for a little over a century—an invisible world waiting to be revealed.\n\nAntonie van Leeuwenhoek, sometimes hailed as \"the Father of Microbiology,\" is typically credited as the first person to have created microscopes powerful enough to view microbes (**[Figure 2.9](#page-60-0)**). Born in the city of Delft in the Dutch Republic, van Leeuwenhoek began his career selling fabrics. However, he later became interested in lens making (perhaps to look at threads) and his innovative techniques produced microscopes that allowed him to observe microorganisms as no one had before. In 1674, he described his observations of single-celled organisms, whose existence was previously unknown, in a series of letters to the Royal Society of London. His report was initially met with skepticism, but his claims were soon verified and he became something of a celebrity in the scientific community. \n \n \n \n**Figure 2.9** (a) Antonie van Leeuwenhoek (1632–1723) is credited as being the first person to observe microbes, including bacteria, which he called \"animalcules\" and \"wee little beasties.\" (b) Even though van Leeuwenhoek's microscopes were simple microscopes (as seen in this replica), they were more powerful and provided better resolution than the compound microscopes of his day. (c) Though more famous for developing the telescope, Galileo Galilei (1564–1642) was also one of the pioneers of microscopy. (credit b: modification of work by \"Wellcome Images\"/Wikimedia Commons) \nWhile van Leeuwenhoek is credited with the discovery of microorganisms, others before him had contributed to the development of the microscope. These included eyeglass makers in the Netherlands in the late 1500s, as well as the Italian astronomer Galileo Galilei, who used a **compound microscope** to examine insect parts (**[Figure 2.9](#page-60-0)**). Whereas van Leeuwenhoek used a **simple microscope,** in which light is passed through just one lens, Galileo's compound microscope was more sophisticated, passing light through two sets of lenses. \nVan Leeuwenhoek's contemporary, the Englishman Robert Hooke (1635–1703), also made important contributions to microscopy, publishing in his book *Micrographia* (1665) many observations using compound microscopes. Viewing a thin sample of cork through his microscope, he was the first to observe the structures that we now know as cells (**[Figure 2.10](#page-60-1)**). Hooke described these structures as resembling \"Honey-comb,\" and as \"small Boxes or Bladders of Air,\" noting that each \"Cavern, Bubble, or Cell\" is distinct from the others (in Latin, \"cell\" literally means \"small room\"). They likely appeared to Hooke to be filled with air because the cork cells were dead, with only the rigid cell walls providing the structure. \n \n**Figure 2.10** Robert Hooke used his (a) compound microscope to view (b) cork cells. Both of these engravings are from his seminal work *Micrographia*, published in 1665. \n \n- Explain the difference between simple and compound microscopes.\n- Compare and contrast the contributions of van Leeuwenhoek, Hooke, and Galileo to early microscopy. \n#### **Micro Connections** \n#### **Who Invented the Microscope?** \nWhile Antonie van Leeuwenhoek and Robert Hooke generally receive much of the credit for early advances in microscopy, neither can claim to be the inventor of the microscope. Some argue that this designation should belong to Hans and Zaccharias Janssen, Dutch spectacle-makers who may have invented the telescope, the simple microscope, and the compound microscope during the late 1500s or early 1600s (**[Figure 2.11](#page-62-1)**). Unfortunately, little is known for sure about the Janssens, not even the exact dates of their births and deaths. The Janssens were secretive about their work and never published. It is also possible that the Janssens did not invent anything at all; their neighbor, Hans Lippershey, also developed microscopes and telescopes during the same time frame, and he is often credited with inventing the telescope. The historical records from the time are as fuzzy and imprecise as the images viewed through those early lenses, and any archived records have been lost over the centuries. \nBy contrast, van Leeuwenhoek and Hooke can thank ample documentation of their work for their respective legacies. Like Janssen, van Leeuwenhoek began his work in obscurity, leaving behind few records. However, his friend, the prominent physician Reinier de Graaf, wrote a letter to the editor of the *Philosophical Transactions of the Royal Society of London* calling attention to van Leeuwenhoek's powerful microscopes. From 1673 onward, van Leeuwenhoek began regularly submitting letters to the Royal Society detailing his observations. In 1674, his report describing single-celled organisms produced controversy in the scientific community, but his observations were soon confirmed when the society sent a delegation to investigate his findings. He subsequently enjoyed considerable celebrity, at one point even entertaining a visit by the czar of Russia. \nSimilarly, Robert Hooke had his observations using microscopes published by the Royal Society in a book called *Micrographia* in 1665. The book became a bestseller and greatly increased interest in microscopy throughout much of Europe. \n \n**Figure 2.11** Zaccharias Janssen, along with his father Hans, may have invented the telescope, the simple microscope, and the compound microscope during the late 1500s or early 1600s. The historical evidence is inconclusive.",
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"Header 2": "Peering Into the Invisible World",
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"page_content": "#### **Learning Objectives** \n- Identify and describe the parts of a brightfield microscope\n- Calculate total magnification for a compound microscope\n- Describe the distinguishing features and typical uses for various types of light microscopes, electron microscopes, and scanning probe microscopes \nThe early pioneers of microscopy opened a window into the invisible world of microorganisms. But microscopy continued to advance in the centuries that followed. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes that leveraged nonvisible light, such as fluorescence microscopy, which uses an ultraviolet light source, and electron microscopy, which uses shortwavelength electron beams. These advances led to major improvements in magnification, resolution, and contrast. By comparison, the relatively rudimentary microscopes of van Leeuwenhoek and his contemporaries were far less powerful than even the most basic microscopes in use today. In this section, we will survey the broad range of modern microscopic technology and common applications for each type of microscope.\n\nMany types of microscopes fall under the category of light microscopes, which use light to visualize images. Examples of light microscopes include brightfield microscopes, darkfield microscopes, phase-contrast microscopes, differential interference contrast microscopes, fluorescence microscopes, confocal scanning laser microscopes, and two-photon microscopes. These various types of light microscopes can be used to complement each other in diagnostics and research. \n#### **Brightfield Microscopes** \nThe **brightfield microscope**, perhaps the most commonly used type of microscope, is a compound microscope with two or more lenses that produce a dark image on a bright background. Some brightfield microscopes are **monocular** (having a single eyepiece), though most newer brightfield microscopes are **binocular** (having two eyepieces), like the one shown in **[Figure 2.12](#page-63-0)**; in either case, each eyepiece contains a lens called an **ocular lens**. The ocular lenses typically magnify images 10 times (10⨯). At the other end of the body tube are a set of **objective lenses** on a rotating nosepiece. The magnification of these objective lenses typically ranges from 4⨯ to 100⨯, with the magnification for each lens designated on the metal casing of the lens. The ocular and objective lenses work together to create a magnified image. The **total magnification** is the product of the ocular magnification times the objective magnification: \nocular magnificatio × objective magnificatio \nFor example, if a 40⨯ objective lens is selected and the ocular lens is 10⨯, the total magnification would be \n(40×)(10×) = 400× \n \n**Figure 2.12** Components of a typical brightfield microscope. \nThe item being viewed is called a specimen. The specimen is placed on a glass slide, which is then clipped into place on the **stage** (a platform) of the microscope. Once the slide is secured, the specimen on the slide is positioned over the light using the **x-y mechanical stage knobs**. These knobs move the slide on the surface of the stage, but do not raise or lower the stage. Once the specimen is centered over the light, the stage position can be raised or lowered to focus the image. The **coarse focusing knob** is used for large-scale movements with 4⨯ and 10⨯ objective lenses; the **fine focusing knob** is used for small-scale movements, especially with 40⨯ or 100⨯ objective lenses. \nWhen images are magnified, they become dimmer because there is less light per unit area of image. Highly magnified images produced by microscopes, therefore, require intense lighting. In a brightfield microscope, this light is provided by an **illuminator**, which is typically a high-intensity bulb below the stage. Light from the illuminator passes up through **condenser lens** (located below the stage), which focuses all of the light rays on the specimen to maximize illumination. The position of the condenser can be optimized using the attached condenser focus knob; once the optimal distance is established, the condenser should not be moved to adjust the brightness. If less-than-maximal light levels are needed, the amount of light striking the specimen can be easily adjusted by opening or closing a **diaphragm** between the condenser and the specimen. In some cases, brightness can also be adjusted using the **rheostat**, a dimmer switch that controls the intensity of the illuminator. \nA brightfield microscope creates an image by directing light from the illuminator at the specimen; this light is differentially transmitted, absorbed, reflected, or refracted by different structures. Different colors can behave differently as they interact with **chromophores** (pigments that absorb and reflect particular wavelengths of light) in parts of the specimen. Often, chromophores are artificially added to the specimen using stains, which serve to increase contrast and resolution. In general, structures in the specimen will appear darker, to various extents, than the bright background, creating maximally sharp images at magnifications up to about 1000⨯. Further magnification would create a larger image, but without increased resolution. This allows us to see objects as small as bacteria, which are visible at about 400⨯ or so, but not smaller objects such as viruses. \nAt very high magnifications, resolution may be compromised when light passes through the small amount of air between the specimen and the lens. This is due to the large difference between the refractive indices of air and glass; the air scatters the light rays before they can be focused by the lens. To solve this problem, a drop of oil can be used to fill the space between the specimen and an **oil immersion lens**, a special lens designed to be used with immersion oils. Since the oil has a refractive index very similar to that of glass, it increases the maximum angle at which light leaving the specimen can strike the lens. This increases the light collected and, thus, the resolution of the image (**[Figure](#page-64-0) [2.13](#page-64-0)**). A variety of oils can be used for different types of light. \n \n**Figure 2.13** (a) Oil immersion lenses like this one are used to improve resolution. (b) Because immersion oil and glass have very similar refractive indices, there is a minimal amount of refraction before the light reaches the lens. Without immersion oil, light scatters as it passes through the air above the slide, degrading the resolution of the image. \n#### **Micro Connections** \n#### **Microscope Maintenance: Best Practices** \nEven a very powerful microscope cannot deliver high-resolution images if it is not properly cleaned and maintained. Since lenses are carefully designed and manufactured to refract light with a high degree of precision, even a slightly dirty or scratched lens will refract light in unintended ways, degrading the image of the specimen. In addition, microscopes are rather delicate instruments, and great care must be taken to avoid damaging parts and surfaces. Among other things, proper care of a microscope includes the following: \n- cleaning the lenses with lens paper\n- not allowing lenses to contact the slide (e.g., by rapidly changing the focus)\n- protecting the bulb (if there is one) from breakage\n- not pushing an objective into a slide\n- not using the coarse focusing knob when using the 40⨯ or greater objective lenses\n- only using immersion oil with a specialized oil objective, usually the 100⨯ objective\n- cleaning oil from immersion lenses after using the microscope\n- cleaning any oil accidentally transferred from other lenses\n- covering the microscope or placing it in a cabinet when not in use \n#### **Link to Learning** \n \nVisit the online resources linked below for simulations and demonstrations involving the use of microscopes. Keep in mind that execution of specific techniques and procedures can vary depending on the specific instrument you are using. Thus, it is important to learn and practice with an actual microscope in a laboratory setting under expert supervision. \n- University of Delaware's **[Virtual Microscope \\(https://www.openstax.org/l/](https://www.openstax.org/l/22virtualsim) [22virtualsim\\)](https://www.openstax.org/l/22virtualsim)**\n- St. John's University **[Microscope Tutorials \\(https://www.openstax.org/l/](https://www.openstax.org/l/22microtut) [22microtut\\)](https://www.openstax.org/l/22microtut)** \n#### **Darkfield Microscopy** \nA **darkfield microscope** is a brightfield microscope that has a small but significant modification to the condenser. A small, opaque disk (about 1 cm in diameter) is placed between the illuminator and the condenser lens. This opaque light stop, as the disk is called, blocks most of the light from the illuminator as it passes through the condenser on its way to the objective lens, producing a hollow cone of light that is focused on the specimen. The only light that reaches the objective is light that has been refracted or reflected by structures in the specimen. The resulting image typically shows bright objects on a dark background (**[Figure 2.14](#page-66-0)**). \n \n**Figure 2.14** An opaque light stop inserted into a brightfield microscope is used to produce a darkfield image. The light stop blocks light traveling directly from the illuminator to the objective lens, allowing only light reflected or refracted off the specimen to reach the eye. \nDarkfield microscopy can often create high-contrast, high-resolution images of specimens without the use of stains, which is particularly useful for viewing live specimens that might be killed or otherwise compromised by the stains. For example, thin spirochetes like *Treponema pallidum*, the causative agent of syphilis, can be best viewed using a darkfield microscope (**[Figure 2.15](#page-66-1)**). \n \n**Figure 2.15** Use of a darkfield microscope allows us to view living, unstained samples of the spirochete *Treponema pallidum*. Similar to a photographic negative, the spirochetes appear bright against a dark background. (credit: Centers for Disease Control and Prevention) \n \n• Identify the key differences between brightfield and darkfield microscopy. \n#### **Clinical Focus** \n#### **Part 2** \nWound infections like Cindy's can be caused by many different types of bacteria, some of which can spread rapidly with serious complications. Identifying the specific cause is very important to select a medication that can kill or stop the growth of the bacteria. \nAfter calling a local doctor about Cindy's case, the camp nurse sends the sample from the wound to the closest medical laboratory. Unfortunately, since the camp is in a remote area, the nearest lab is small and poorly equipped. A more modern lab would likely use other methods to culture, grow, and identify the bacteria, but in this case, the technician decides to make a wet mount from the specimen and view it under a brightfield microscope. In a wet mount, a small drop of water is added to the slide, and a cover slip is placed over the specimen to keep it in place before it is positioned under the objective lens. \nUnder the brightfield microscope, the technician can barely see the bacteria cells because they are nearly transparent against the bright background. To increase contrast, the technician inserts an opaque light stop above the illuminator. The resulting darkfield image clearly shows that the bacteria cells are spherical and grouped in clusters, like grapes. \n- Why is it important to identify the shape and growth patterns of cells in a specimen?\n- What other types of microscopy could be used effectively to view this specimen? \n*Jump to the [next](#page-84-0) Clinical Focus box. Go back to the [previous](#page-53-2) Clinical Focus box.* \n#### **Phase-Contrast Microscopes** \n**Phase-contrast microscopes** use refraction and interference caused by structures in a specimen to create highcontrast, high-resolution images without staining. It is the oldest and simplest type of microscope that creates an image by altering the wavelengths of light rays passing through the specimen. To create altered wavelength paths, an annular stop is used in the condenser. The annular stop produces a hollow cone of light that is focused on the specimen before reaching the objective lens. The objective contains a phase plate containing a phase ring. As a result, light traveling directly from the illuminator passes through the phase ring while light refracted or reflected by the specimen passes through the plate. This causes waves traveling through the ring to be about one-half of a wavelength out of phase with those passing through the plate. Because waves have peaks and troughs, they can add together (if in phase together) or cancel each other out (if out of phase). When the wavelengths are out of phase, wave troughs will cancel out wave peaks, which is called destructive interference. Structures that refract light then appear dark against a bright background of only unrefracted light. More generally, structures that differ in features such as refractive index will differ in levels of darkness (**[Figure 2.16](#page-68-0)**). \n \n**Figure 2.16** This diagram of a phase-contrast microscope illustrates phase differences between light passing through the object and background. These differences are produced by passing the rays through different parts of a phase plate. The light rays are superimposed in the image plane, producing contrast due to their interference. \nBecause it increases contrast without requiring stains, phase-contrast microscopy is often used to observe live specimens. Certain structures, such as organelles in eukaryotic cells and endospores in prokaryotic cells, are especially well visualized with phase-contrast microscopy (**[Figure 2.17](#page-68-1)**). \n \n**Figure 2.17** This figure compares a brightfield image (left) with a phase-contrast image (right) of the same unstained simple squamous epithelial cells. The cells are in the center and bottom right of each photograph (the irregular item above the cells is acellular debris). Notice that the unstained cells in the brightfield image are almost invisible against the background, whereas the cells in the phase-contrast image appear to glow against the background, revealing far more detail. \n#### **Differential Interference Contrast Microscopes** \n**Differential interference contrast (DIC) microscopes** (also known as Nomarski optics) are similar to phase-contrast \nmicroscopes in that they use interference patterns to enhance contrast between different features of a specimen. In a DIC microscope, two beams of light are created in which the direction of wave movement (polarization) differs. Once the beams pass through either the specimen or specimen-free space, they are recombined and effects of the specimens cause differences in the interference patterns generated by the combining of the beams. This results in high-contrast images of living organisms with a three-dimensional appearance. These microscopes are especially useful in distinguishing structures within live, unstained specimens. (**[Figure 2.18](#page-69-0)**) \n \n**Figure 2.18** A DIC image of *Fonsecaea pedrosoi* grown on modified Leonian's agar. This fungus causes chromoblastomycosis, a chronic skin infection common in tropical and subtropical climates. \n \n• What are some advantages of phase-contrast and DIC microscopy? \n#### **Fluorescence Microscopes** \nA **fluorescence microscope** uses fluorescent chromophores called **fluorochromes**, which are capable of absorbing energy from a light source and then emitting this energy as visible light. Fluorochromes include naturally fluorescent substances (such as chlorophylls) as well as fluorescent stains that are added to the specimen to create contrast. Dyes such as Texas red and FITC are examples of fluorochromes. Other examples include the nucleic acid dyes 4',6' diamidino-2-phenylindole (DAPI) and acridine orange. \nThe microscope transmits an excitation light, generally a form of EMR with a short wavelength, such as ultraviolet or blue light, toward the specimen; the chromophores absorb the excitation light and emit visible light with longer wavelengths. The excitation light is then filtered out (in part because ultraviolet light is harmful to the eyes) so that only visible light passes through the ocular lens. This produces an image of the specimen in bright colors against a dark background. \nFluorescence microscopes are especially useful in clinical microbiology. They can be used to identify pathogens, to find particular species within an environment, or to find the locations of particular molecules and structures within a cell. Approaches have also been developed to distinguish living from dead cells using fluorescence microscopy based upon whether they take up particular fluorochromes. Sometimes, multiple fluorochromes are used on the same specimen to show different structures or features. \nOne of the most important applications of fluorescence microscopy is a technique called **immunofluorescence**, which is used to identify certain disease-causing microbes by observing whether antibodies bind to them. (Antibodies are protein molecules produced by the immune system that attach to specific pathogens to kill or inhibit them.) There are two approaches to this technique: direct immunofluorescence assay (DFA) and indirect immunofluorescence assay (IFA). In DFA, specific antibodies (e.g., those that the target the rabies virus) are stained with a fluorochrome. If the specimen contains the targeted pathogen, one can observe the antibodies binding to the pathogen under the fluorescent microscope. This is called a primary antibody stain because the stained antibodies attach directly to the pathogen. \nIn IFA, secondary antibodies are stained with a fluorochrome rather than primary antibodies. Secondary antibodies do not attach directly to the pathogen, but they do bind to primary antibodies. When the unstained primary antibodies bind to the pathogen, the fluorescent secondary antibodies can be observed binding to the primary antibodies. Thus, the secondary antibodies are attached indirectly to the pathogen. Since multiple secondary antibodies can often attach to a primary antibody, IFA increases the number of fluorescent antibodies attached to the specimen, making it easier visualize features in the specimen (**[Figure 2.19](#page-70-0)**). \n \n**Figure 2.19** (a) A direct immunofluorescent stain is used to visualize *Neisseria gonorrhoeae*, the bacterium that causes gonorrhea. (b) An indirect immunofluorescent stain is used to visualize larvae of *Schistosoma mansoni*, a parasitic worm that causes schistosomiasis, an intestinal disease common in the tropics. (c) In direct immunofluorescence, the stain is absorbed by a primary antibody, which binds to the antigen. In indirect immunofluorescence, the stain is absorbed by a secondary antibody, which binds to a primary antibody, which, in turn, binds to the antigen. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Centers for Disease Control and Prevention) \n \n• Why must fluorochromes be used to examine a specimen under a fluorescence microscope? \n#### **Confocal Microscopes** \nWhereas other forms of light microscopy create an image that is maximally focused at a single distance from the observer (the depth, or z-plane), a **confocal microscope** uses a laser to scan multiple z-planes successively. This produces numerous two-dimensional, high-resolution images at various depths, which can be constructed into a threedimensional image by a computer. As with fluorescence microscopes, fluorescent stains are generally used to increase contrast and resolution. Image clarity is further enhanced by a narrow aperture that eliminates any light that is not from the z-plane. Confocal microscopes are thus very useful for examining thick specimens such as biofilms, which can be examined alive and unfixed (**[Figure 2.20](#page-71-0)**). \n \n**Figure 2.20** Confocal microscopy can be used to visualize structures such as this roof-dwelling cyanobacterium biofilm. (credit: modification of work by American Society for Microbiology) \n#### **Link to Learning** \n \nExplore a rotating three-dimensional **[view \\(https://www.openstax.org/l/](https://www.openstax.org/l/22biofilm3d) [22biofilm3d\\)](https://www.openstax.org/l/22biofilm3d)** of a biofilm as observed under a confocal microscope. After navigating to the webpage, click the \"play\" button to launch the video. \n#### **Two-Photon Microscopes** \nWhile the original fluorescent and confocal microscopes allowed better visualization of unique features in specimens, there were still problems that prevented optimum visualization. The effective sensitivity of fluorescence microscopy when viewing thick specimens was generally limited by out-of-focus flare, which resulted in poor resolution. This limitation was greatly reduced in the confocal microscope through the use of a confocal pinhole to reject out-of-focus background fluorescence with thin (<1 μm), unblurred optical sections. However, even the confocal microscopes lacked the resolution needed for viewing thick tissue samples. These problems were resolved with the development of the **two-photon microscope**, which uses a scanning technique, fluorochromes, and long-wavelength light (such as infrared) to visualize specimens. The low energy associated with the long-wavelength light means that two photons must strike a location at the same time to excite the fluorochrome. The low energy of the excitation light is less damaging to cells, and the long wavelength of the excitation light more easily penetrates deep into thick specimens. This makes the two-photon microscope useful for examining living cells within intact tissues—brain slices, embryos, whole organs, and even entire animals. \nCurrently, use of two-photon microscopes is limited to advanced clinical and research laboratories because of the high costs of the instruments. A single two-photon microscope typically costs between \\$300,000 and \\$500,000, and the lasers used to excite the dyes used on specimens are also very expensive. However, as technology improves, twophoton microscopes may become more readily available in clinical settings. \n \n• What types of specimens are best examined using confocal or two-photon microscopy?\n\nThe maximum theoretical resolution of images created by light microscopes is ultimately limited by the wavelengths of visible light. Most light microscopes can only magnify 1000⨯, and a few can magnify up to 1500⨯, but this does not begin to approach the magnifying power of an **electron microscope (EM)**, which uses short-wavelength electron beams rather than light to increase magnification and resolution. \nElectrons, like electromagnetic radiation, can behave as waves, but with wavelengths of 0.005 nm, they can produce much better resolution than visible light. An EM can produce a sharp image that is magnified up to 100,000⨯. Thus, EMs can resolve subcellular structures as well as some molecular structures (e.g., single strands of DNA); however, electron microscopy cannot be used on living material because of the methods needed to prepare the specimens. \nThere are two basic types of EM: the **transmission electron microscope (TEM)** and the **scanning electron microscope (SEM)** (**[Figure 2.21](#page-72-0)**). The TEM is somewhat analogous to the brightfield light microscope in terms of the way it functions. However, it uses an electron beam from above the specimen that is focused using a magnetic lens (rather than a glass lens) and projected through the specimen onto a detector. Electrons pass through the specimen, and then the detector captures the image (**[Figure 2.22](#page-73-0)**). \n \n**Figure 2.21** A transmission electron microscope (TEM). \n \n**Figure 2.22** Electron microscopes use magnets to focus electron beams similarly to the way that light microscopes use lenses to focus light. \nFor electrons to pass through the specimen in a TEM, the specimen must be extremely thin (20–100 nm thick). The image is produced because of varying opacity in various parts of the specimen. This opacity can be enhanced by staining the specimen with materials such as heavy metals, which are electron dense. TEM requires that the beam and specimen be in a vacuum and that the specimen be very thin and dehydrated. The specific steps needed to prepare a specimen for observation under an EM are discussed in detail in the next section. \nSEMs form images of surfaces of specimens, usually from electrons that are knocked off of specimens by a beam of electrons. This can create highly detailed images with a three-dimensional appearance that are displayed on a monitor (**[Figure 2.23](#page-74-0)**). Typically, specimens are dried and prepared with fixatives that reduce artifacts, such as shriveling, that can be produced by drying, before being sputter-coated with a thin layer of metal such as gold. Whereas transmission electron microscopy requires very thin sections and allows one to see internal structures such as organelles and the interior of membranes, scanning electron microscopy can be used to view the surfaces of larger objects (such as a pollen grain) as well as the surfaces of very small samples (**[Figure 2.24](#page-74-1)**). Some EMs can magnify an image up to 2,000,000⨯. [1] \n1. "JEM-ARM200F Transmission Electron Microscope,\" *JEOL USA Inc*, http://www.jeolusa.com/PRODUCTS/ TransmissionElectronMicroscopes%28TEM%29/200kV/JEM-ARM200F/tabid/663/Default.aspx#195028-specifications. Accessed 8/28/ 2015. \n \n**Figure 2.23** These schematic illustrations compare the components of transmission electron microscopes and scanning electron microscopes. \n \n**Figure 2.24** (a) This TEM image of cells in a biofilm shows well-defined internal structures of the cells because of varying levels of opacity in the specimen. (b) This color-enhanced SEM image of the bacterium *Staphylococcus aureus* illustrates the ability of scanning electron microscopy to render three-dimensional images of the surface structure of cells. (credit a: modification of work by American Society for Microbiology; credit b: modification of work by Centers for Disease Control and Prevention) \n \n- What are some advantages and disadvantages of electron microscopy, as opposed to light microscopy, for examining microbiological specimens?\n- What kinds of specimens are best examined using TEM? SEM? \n#### **Micro Connections** \n#### **Using Microscopy to Study Biofilms** \nA biofilm is a complex community of one or more microorganism species, typically forming as a slimy coating attached to a surface because of the production of an extrapolymeric substance (EPS) that attaches to a surface or at the interface between surfaces (e.g., between air and water). In nature, biofilms are abundant and frequently occupy complex niches within ecosystems (**[Figure 2.25](#page-75-0)**). In medicine, biofilms can coat medical devices and exist within the body. Because they possess unique characteristics, such as increased resistance against the immune system and to antimicrobial drugs, biofilms are of particular interest to microbiologists and clinicians alike. \nBecause biofilms are thick, they cannot be observed very well using light microscopy; slicing a biofilm to create a thinner specimen might kill or disturb the microbial community. Confocal microscopy provides clearer images of biofilms because it can focus on one z-plane at a time and produce a three-dimensional image of a thick specimen. Fluorescent dyes can be helpful in identifying cells within the matrix. Additionally, techniques such as immunofluorescence and fluorescence in situ hybridization (FISH), in which fluorescent probes are used to bind to DNA, can be used. \nElectron microscopy can be used to observe biofilms, but only after dehydrating the specimen, which produces undesirable artifacts and distorts the specimen. In addition to these approaches, it is possible to follow water currents through the shapes (such as cones and mushrooms) of biofilms, using video of the movement of fluorescently coated beads (**[Figure 2.26](#page-76-0)**). \n \n**Figure 2.25** A biofilm forms when planktonic (free-floating) bacteria of one or more species adhere to a surface, produce slime, and form a colony. (credit: Public Library of Science) \n \n**Figure 2.26** In this image, multiple species of bacteria grow in a biofilm on stainless steel (stained with DAPI for epifluorescence miscroscopy). (credit: Ricardo Murga, Rodney Donlan)\n\nA **scanning probe microscope** does not use light or electrons, but rather very sharp probes that are passed over the surface of the specimen and interact with it directly. This produces information that can be assembled into images with magnifications up to 100,000,000⨯. Such large magnifications can be used to observe individual atoms on surfaces. To date, these techniques have been used primarily for research rather than for diagnostics. \nThere are two types of scanning probe microscope: the **scanning tunneling microscope (STM)** and the **atomic force microscope (AFM)**. An STM uses a probe that is passed just above the specimen as a constant voltage bias creates the potential for an electric current between the probe and the specimen. This current occurs via quantum tunneling of electrons between the probe and the specimen, and the intensity of the current is dependent upon the distance between the probe and the specimen. The probe is moved horizontally above the surface and the intensity of the current is measured. Scanning tunneling microscopy can effectively map the structure of surfaces at a resolution at which individual atoms can be detected. \nSimilar to an STM, AFMs have a thin probe that is passed just above the specimen. However, rather than measuring variations in the current at a constant height above the specimen, an AFM establishes a constant current and measures variations in the height of the probe tip as it passes over the specimen. As the probe tip is passed over the specimen, forces between the atoms (van der Waals forces, capillary forces, chemical bonding, electrostatic forces, and others) cause it to move up and down. Deflection of the probe tip is determined and measured using Hooke's law of elasticity, and this information is used to construct images of the surface of the specimen with resolution at the atomic level (**[Figure 2.27](#page-77-0)**). \n**[Figure 2.28](#page-78-0)**, **[Figure 2.29](#page-79-0)**, and **[Figure 2.30](#page-79-1)** summarize the microscopy techniques for light microscopes, electron microscopes, and scanning probe microscopes, respectively. \n \n**Figure 2.27** STMs and AFMs allow us to view images at the atomic level. (a) This STM image of a pure gold surface shows individual atoms of gold arranged in columns. (b) This AFM image shows long, strand-like molecules of nanocellulose, a laboratory-created substance derived from plant fibers. (credit a: modification of work by \"Erwinrossen\"/Wikimedia Commons) \n \n- Which has higher magnification, a light microscope or a scanning probe microscope?\n- Name one advantage and one limitation of scanning probe microscopy. \n| monly used in a wide variety of laboratory applications as the ard microscope; produces an image on a bright background. Inple: Bacillus sp. showing endospores. Inspective assessment of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of the state of | ASM Fight Engage Smith |\n|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| darker background; especially useful for viewing live mens. Inple: Borrelia burgdorferi refraction and interference caused by structures in the men to create high-contrast, high-resolution images without ng, making it useful for viewing live specimens, and ures such as endospores and organelles. Inple: Pseudomonas sp. interference patterns to enhance contrast between different | 1 13/1- |\n| men to create high-contrast, high-resolution images without ng, making it useful for viewing live specimens, and ures such as endospores and organelles. aple: Pseudomonas sp. interference patterns to enhance contrast between different | 1 13/1/2 |\n| | |\n| res of a specimen to produce high-contrast images of living issues with a three-dimensional appearance, making it cially useful in distinguishing structures within live, unstained mens; images viewed reveal detailed structures within cells. Inple: Escherichia coli O157:H7 | |\n| fluorescent stains to produce an image; can be used to fy pathogens, to find particular species, to distinguish living dead cells, or to find locations of particular molecules within also used for immunofluorescence. Iple: P. putida stained with fluorescent dyes to visualize the alle. | ASM Microbel dizary ongo(Shiore |\n| a laser to scan mutiple z-planes successively, producing rous two-dimensional, high-resolution images at various s that can be constructed into a three-dimensional image computer, making this useful for examining thick specimens as biofilms. aple: Escherichia coli stained with acridine orange dye to the nucleoid regions of the cells. | Marie Control |\n| a scanning technique, fluorochromes, and long-wavelength such as infrared) to penetrate deep into thick specimens as biofilms. | |\n| | a laser to scan mutiple z-planes successively, producing rous two-dimensional, high-resolution images at various s that can be constructed into a three-dimensional image computer, making this useful for examining thick specimens as biofilms. **aple: Escherichia coli** stained with acridine orange dye to the nucleoid regions of the cells. **a scanning technique, fluorochromes, and long-wavelength such as infrared) to penetrate deep into thick specimens | \n**Figure 2.28** (credit \"Brightfield\": modification of work by American Society for Microbiology; credit \"Darkfield\": modification of work by American Society for Microbiology; credit \"Phase contrast\": modification of work by American Society for Microbiology; credit \"DIC\": modification of work by American Society for Microbiology; credit \"Fluorescence\": modification of work by American Society for Microbiology; credit \"Confocal\": modification of work by American Society for Microbiology; credit \"Two-photon\": modification of work by Alberto Diaspro, Paolo Bianchini, Giuseppe Vicidomini, Mario Faretta, Paola Ramoino, Cesare Usai) \n| ELECTRON MICROSCOPES Magnification: 20–100,000× or more Use electron beams focused with magnets to produce an image. | | | | |\n|----------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|--|--|\n| Microscope Type | Key Uses | Sample Images | | |\n| Transmission
(TEM) | Uses electron beams that pass through a specimen to visualize small images; useful to observe small, thin specimens such as tissue sections and subcellular structures. Example: Ebola virus | | | |\n| Scanning (SEM) | Uses electron beams to visualize surfaces; useful to observe the three-dimensional surface details of specimens. Example: Campylobactor jejuni | | | | \n**Figure 2.29** (credit \"TEM\": modification of work by American Society for Microbiology; credit \"SEM\": modification of work by American Society for Microbiology) \n| | SCANNING PROBE MICROSCOPES Magnification: 100–100,000,000× or more Use very short probes that are passed over the surface of the specimen and interact with it directly. | | | | | |\n|-----------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|--|--|--|--|\n| Microscope Type | Key Uses | Sample Images | | | | |\n| Scanning
tunneling (STM) | Uses a probe passed horizontally at a constant distance just above the specimen while the intensity of the current is measured; can map the structure of surfaces at the atomic level; works best on conducting materials but can also be used to examine organic materials such as DNA, if fixed on a surface. Example: Image of surface reconstruction on a clean gold [Au(100)] surface, as visualized using scanning tunneling microscopy. | | | | | |\n| Atomic force (AFM) | Can be used in several ways, including using a laser focused on a cantilever to measure the bending of the tip or a probe passed above the specimen while the height needed to maintain a constant current is measured; useful to observe specimens at the atomic level and can be more easily used with nonconducting samples. Example: AFM height image of carboxymethylated nanocellulose adsorbed on a silica surface. | | | | | | \n**Figure 2.30**",
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"page_content": "#### **Learning Objectives** \n- Differentiate between simple and differential stains\n- Describe the unique features of commonly used stains\n- Explain the procedures and name clinical applications for Gram, endospore, acid-fast, negative capsule, and flagella staining \nIn their natural state, most of the cells and microorganisms that we observe under the microscope lack color and contrast. This makes it difficult, if not impossible, to detect important cellular structures and their distinguishing characteristics without artificially treating specimens. We have already alluded to certain techniques involving stains and fluorescent dyes, and in this section we will discuss specific techniques for sample preparation in greater detail. Indeed, numerous methods have been developed to identify specific microbes, cellular structures, DNA sequences, or indicators of infection in tissue samples, under the microscope. Here, we will focus on the most clinically relevant techniques.\n\nIn clinical settings, light microscopes are the most commonly used microscopes. There are two basic types of preparation used to view specimens with a light microscope: wet mounts and fixed specimens. \nThe simplest type of preparation is the **wet mount**, in which the specimen is placed on the slide in a drop of liquid. Some specimens, such as a drop of urine, are already in a liquid form and can be deposited on the slide using a dropper. Solid specimens, such as a skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid used is simply water, but often stains are added to enhance contrast. Once the liquid has been added to the slide, a coverslip is placed on top and the specimen is ready for examination under the microscope. \nThe second method of preparing specimens for light microscopy is **fixation**. The \"fixing\" of a sample refers to the process of attaching cells to a slide. Fixation is often achieved either by heating (heat fixing) or chemically treating the specimen. In addition to attaching the specimen to the slide, fixation also kills microorganisms in the specimen, stopping their movement and metabolism while preserving the integrity of their cellular components for observation. \nTo heat-fix a sample, a thin layer of the specimen is spread on the slide (called a **smear**), and the slide is then briefly heated over a heat source (**[Figure 2.31](#page-81-0)**). Chemical fixatives are often preferable to heat for tissue specimens. Chemical agents such as acetic acid, ethanol, methanol, formaldehyde (formalin), and glutaraldehyde can denature proteins, stop biochemical reactions, and stabilize cell structures in tissue samples (**[Figure 2.31](#page-81-0)**). \n \n \n \n**Figure 2.31** (a) A specimen can be heat-fixed by using a slide warmer like this one. (b) Another method for heatfixing a specimen is to hold a slide with a smear over a microincinerator. (c) This tissue sample is being fixed in a solution of formalin (also known as formaldehyde). Chemical fixation kills microorganisms in the specimen, stopping degradation of the tissues and preserving their structure so that they can be examined later under the microscope. (credit a: modification of work by Nina Parker; credit b: modification of work by Nina Parker; credit c: modification of work by \"University of Bristol\"/YouTube) \nIn addition to fixation, **staining** is almost always applied to color certain features of a specimen before examining it under a light microscope. Stains, or dyes, contain salts made up of a positive ion and a negative ion. Depending on the type of dye, the positive or the negative ion may be the chromophore (the colored ion); the other, uncolored ion is called the counterion. If the chromophore is the positively charged ion, the stain is classified as a **basic dye**; if the negative ion is the chromophore, the stain is considered an **acidic dye**. \nDyes are selected for staining based on the chemical properties of the dye and the specimen being observed, which determine how the dye will interact with the specimen. In most cases, it is preferable to use a **positive stain**, a dye that will be absorbed by the cells or organisms being observed, adding color to objects of interest to make them stand out against the background. However, there are scenarios in which it is advantageous to use a **negative stain**, which is absorbed by the background but not by the cells or organisms in the specimen. Negative staining produces an outline or silhouette of the organisms against a colorful background (**[Figure 2.32](#page-81-1)**). \n \n \n \n**Figure 2.32** (a) These *Bacillus anthracis* cells have absorbed crystal violet, a basic positive stain. (b) This specimen of *Spinoloricus*, a microscopic marine organism, has been stained with rose bengal, a positive acidic stain. (c) These *B. megaterium* appear to be white because they have not absorbed the negative red stain applied to the slide. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Roberto Danovaro, Antonio Pusceddu, Cristina Gambi, Iben Heiner, Reinhardt Mobjerg Kristensen; credit c: modification of work by Anh-Hue Tu) \nBecause cells typically have negatively charged cell walls, the positive chromophores in basic dyes tend to stick to the cell walls, making them positive stains. Thus, commonly used basic dyes such as basic fuchsin, crystal violet, malachite green, methylene blue, and safranin typically serve as positive stains. On the other hand, the negatively charged chromophores in acidic dyes are repelled by negatively charged cell walls, making them negative stains. Commonly used acidic dyes include acid fuchsin, eosin, and rose bengal. **[Figure 2.40](#page-88-0)** provides more detail. \nSome staining techniques involve the application of only one dye to the sample; others require more than one dye. In **simple staining**, a single dye is used to emphasize particular structures in the specimen. A simple stain will generally make all of the organisms in a sample appear to be the same color, even if the sample contains more than one type of organism. In contrast, **differential staining** distinguishes organisms based on their interactions with multiple stains. In other words, two organisms in a differentially stained sample may appear to be different colors. Differential staining techniques commonly used in clinical settings include Gram staining, acid-fast staining, endospore staining, flagella staining, and capsule staining. **[Figure 2.41](#page-89-0)** provides more detail on these differential staining techniques. \n \n- Explain why it is important to fix a specimen before viewing it under a light microscope.\n- What types of specimens should be chemically fixed as opposed to heat-fixed?\n- Why might an acidic dye react differently with a given specimen than a basic dye?\n- Explain the difference between a positive stain and a negative stain.\n- Explain the difference between simple and differential staining.\n\nThe **Gram stain procedure** is a differential staining procedure that involves multiple steps. It was developed by Danish microbiologist Hans Christian Gram in 1884 as an effective method to distinguish between bacteria with different types of cell walls, and even today it remains one of the most frequently used staining techniques. The steps of the Gram stain procedure are listed below and illustrated in **[Figure 2.33](#page-83-0)**. \n- 1. First, crystal violet, a **primary stain**, is applied to a heat-fixed smear, giving all of the cells a purple color.\n- 2. Next, Gram's iodine, a **mordant**, is added. A mordant is a substance used to set or stabilize stains or dyes; in this case, Gram's iodine acts like a trapping agent that complexes with the crystal violet, making the crystal violet–iodine complex clump and stay contained in thick layers of peptidoglycan in the cell walls.\n- 3. Next, a **decolorizing agent** is added, usually ethanol or an acetone/ethanol solution. Cells that have thick peptidoglycan layers in their cell walls are much less affected by the decolorizing agent; they generally retain the crystal violet dye and remain purple. However, the decolorizing agent more easily washes the dye out of cells with thinner peptidoglycan layers, making them again colorless.\n- 4. Finally, a secondary **counterstain**, usually safranin, is added. This stains the decolorized cells pink and is less noticeable in the cells that still contain the crystal violet dye. \n| | Gram stain process | | | |\n|-----------------------------------------------------------------------------|---------------------------------------------------------------------------------------------|---------------|---------------|--|\n| Gram staining steps | Cell effects | Gram-positive | Gram-negative | |\n| Step 1 Crystal violet primary stain added to specimen smear. | Stains cells purple or blue. | | | |\n| Step 2 Iodine mordant makes dye less soluble so it adheres to cell walls. | Cells remain purple or blue. | | | |\n| Step 3 Alcohol decolorizer washes away stain from gram-negative cell walls. | Gram-positive cells
remain purple or blue.
Gram-negative cells
are colorless. | 8 | | |\n| Step 4 Safranin counterstain allows dye adherance to gram-negative cells. | Gram-positive cells
remain purple or blue.
Gram-negative cells
appear pink or red. | | | | \n**Figure 2.33** Gram-staining is a differential staining technique that uses a primary stain and a secondary counterstain to distinguish between gram-positive and gram-negative bacteria. \nThe purple, crystal-violet stained cells are referred to as gram-positive cells, while the red, safranin-dyed cells are gram-negative (**[Figure 2.34](#page-84-1)**). However, there are several important considerations in interpreting the results of a Gram stain. First, older bacterial cells may have damage to their cell walls that causes them to appear gramnegative even if the species is gram-positive. Thus, it is best to use fresh bacterial cultures for Gram staining. Second, errors such as leaving on decolorizer too long can affect the results. In some cases, most cells will appear grampositive while a few appear gram-negative (as in **[Figure 2.34](#page-84-1)**). This suggests damage to the individual cells or that decolorizer was left on for too long; the cells should still be classified as gram-positive if they are all the same species rather than a mixed culture. \nBesides their differing interactions with dyes and decolorizing agents, the chemical differences between grampositive and gram-negative cells have other implications with clinical relevance. For example, Gram staining can help clinicians classify bacterial pathogens in a sample into categories associated with specific properties. Gram-negative bacteria tend to be more resistant to certain antibiotics than gram-positive bacteria. We will discuss this and other applications of Gram staining in more detail in later chapters. \n \n**Figure 2.34** In this specimen, the gram-positive bacterium *Staphylococcus aureus* retains crystal violet dye even after the decolorizing agent is added. Gram-negative *Escherichia coli*, the most common Gram stain quality-control bacterium, is decolorized, and is only visible after the addition of the pink counterstain safranin. (credit: modification of work by Nina Parker) \n \n- Explain the role of Gram's iodine in the Gram stain procedure.\n- Explain the role of alcohol in the Gram stain procedure.\n- What color are gram-positive and gram-negative cells, respectively, after the Gram stain procedure? \n#### **Clinical Focus** \n#### **Part 3** \nViewing Cindy's specimen under the darkfield microscope has provided the technician with some important clues about the identity of the microbe causing her infection. However, more information is needed to make a conclusive diagnosis. The technician decides to make a Gram stain of the specimen. This technique is commonly used as an early step in identifying pathogenic bacteria. After completing the Gram stain procedure, the technician views the slide under the brightfield microscope and sees purple, grape-like clusters of spherical cells (**[Figure 2.35](#page-85-0)**). \n- Are these bacteria gram-positive or gram-negative?\n- What does this reveal about their cell walls? \n*Jump to the [next](#page-92-0) Clinical Focus box. Go back to the [previous](#page-67-0) Clinical Focus box.* \n \n**Figure 2.35** (credit: modification of work by American Society for Microbiology)\n\nAcid-fast staining is another commonly used, differential staining technique that can be an important diagnostic tool. An **acid-fast stain** is able to differentiate two types of gram-positive cells: those that have waxy mycolic acids in their cell walls, and those that do not. Two different methods for acid-fast staining are the **Ziehl-Neelsen technique** and the **Kinyoun technique**. Both use carbolfuchsin as the primary stain. The waxy, acid-fast cells retain the carbolfuchsin even after a decolorizing agent (an acid-alcohol solution) is applied. A secondary counterstain, methylene blue, is then applied, which renders non–acid-fast cells blue. \nThe fundamental difference between the two carbolfuchsin-based methods is whether heat is used during the primary staining process. The Ziehl-Neelsen method uses heat to infuse the carbolfuchsin into the acid-fast cells, whereas the Kinyoun method does not use heat. Both techniques are important diagnostic tools because a number of specific diseases are caused by acid-fast bacteria (AFB). If AFB are present in a tissue sample, their red or pink color can be seen clearly against the blue background of the surrounding tissue cells (**[Figure 2.36](#page-86-0)**). \n \n• Why are acid-fast stains useful? \n#### **Micro Connections** \n#### **Using Microscopy to Diagnose Tuberculosis** \n*Mycobacterium tuberculosis*, the bacterium that causes tuberculosis, can be detected in specimens based on the presence of acid-fast bacilli. Often, a smear is prepared from a sample of the patient's sputum and then stained using the Ziehl-Neelsen technique (**[Figure 2.36](#page-86-0)**). If acid-fast bacteria are confirmed, they are generally cultured to make a positive identification. Variations of this approach can be used as a first step in determining whether *M. tuberculosis* or other acid-fast bacteria are present, though samples from elsewhere in the body (such as urine) may contain other *Mycobacterium* species. \nAn alternative approach for determining the presence of *M. tuberculosis* is immunofluorescence. In this technique, fluorochrome-labeled antibodies bind to *M. tuberculosis*, if present. Antibody-specific fluorescent dyes can be used to view the mycobacteria with a fluorescence microscope. \n \n**Figure 2.36** Ziehl-Neelsen staining has rendered these *Mycobacterium tuberculosis* cells red and the surrounding growth indicator medium blue. (credit: modification of work by American Society for Microbiology)\n\nCertain bacteria and yeasts have a protective outer structure called a capsule. Since the presence of a capsule is directly related to a microbe's virulence (its ability to cause disease), the ability to determine whether cells in a sample have capsules is an important diagnostic tool. Capsules do not absorb most basic dyes; therefore, a negative staining technique (staining around the cells) is typically used for **capsule staining**. The dye stains the background but does not penetrate the capsules, which appear like halos around the borders of the cell. The specimen does not need to be heat-fixed prior to negative staining. \nOne common negative staining technique for identifying encapsulated yeast and bacteria is to add a few drops of India ink or nigrosin to a specimen. Other capsular stains can also be used to negatively stain encapsulated cells (**[Figure](#page-86-1) [2.37](#page-86-1)**). Alternatively, positive and negative staining techniques can be combined to visualize capsules: The positive stain colors the body of the cell, and the negative stain colors the background but not the capsule, leaving halo around each cell. \n \n \n**Figure 2.37** (a) India-ink was used to stain the background around these cells of the yeast *Cryptococcus neoformans*. The halos surrounding the cells are the polysaccharide capsules. (b) Crystal violet and copper sulfate dyes cannot penetrate the encapsulated *Bacillus* cells in this negatively stained sample. Encapsulated cells appear to have a light-blue halo. (credit a: modification of work by American Society for Microbiology; credit b: modification of work by American Society for Microbiology) \n \n• How does negative staining help us visualize capsules? \n#### **Endospore Staining** \nEndospores are structures produced within certain bacterial cells that allow them to survive harsh conditions. Gram staining alone cannot be used to visualize endospores, which appear clear when Gram-stained cells are viewed. **Endospore staining** uses two stains to differentiate endospores from the rest of the cell. The Schaeffer-Fulton method (the most commonly used endospore-staining technique) uses heat to push the primary stain (malachite green) into the endospore. Washing with water decolorizes the cell, but the endospore retains the green stain. The cell is then counterstained pink with safranin. The resulting image reveals the shape and location of endospores, if they are present. The green endospores will appear either within the pink vegetative cells or as separate from the pink cells altogether. If no endospores are present, then only the pink vegetative cells will be visible (**[Figure 2.38](#page-87-0)**). \n \n**Figure 2.38** A stained preparation of *Bacillus subtilis* showing endospores as green and the vegetative cells as pink. (credit: modification of work by American Society for Microbiology) \nEndospore-staining techniques are important for identifying *Bacillus* and *Clostridium*, two genera of endosporeproducing bacteria that contain clinically significant species. Among others, *B. anthracis* (which causes anthrax) has been of particular interest because of concern that its spores could be used as a bioterrorism agent. *C. difficile* is a particularly important species responsible for the typically hospital-acquired infection known as \"C. diff.\" \n \n• Is endospore staining an example of positive, negative, or differential staining?\n\nFlagella (singular: flagellum) are tail-like cellular structures used for locomotion by some bacteria, archaea, and eukaryotes. Because they are so thin, flagella typically cannot be seen under a light microscope without a specialized **flagella staining** technique. Flagella staining thickens the flagella by first applying mordant (generally tannic acid, but sometimes potassium alum), which coats the flagella; then the specimen is stained with pararosaniline (most commonly) or basic fuchsin (**[Figure 2.39](#page-88-1)**). \n \n**Figure 2.39** A flagella stain of *Bacillus cereus*, a common cause of foodborne illness, reveals that the cells have numerous flagella, used for locomotion. (credit: modification of work by Centers for Disease Control and Prevention) \nThough flagella staining is uncommon in clinical settings, the technique is commonly used by microbiologists, since the location and number of flagella can be useful in classifying and identifying bacteria in a sample. When using this technique, it is important to handle the specimen with great care; flagella are delicate structures that can easily be damaged or pulled off, compromising attempts to accurately locate and count the number of flagella. \n| | SIMPLE STAINS | | | | |\n|--------------------|--------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------|---------------|--|\n| Stain Type | Specific Dyes | Purpose | Outcome | Sample Images | |\n| Basic
stains | Methylene blue,
crystal violet,
malachite green,
basic fuchsin,
carbolfuchsin,
safranin | Stain negatively
charged molecules
and structures,
such as nucleic
acids and proteins | Positive stain | | |\n| Acidic
stains | Eosin,
acid fuchsin,
rose bengal,
Congo red | Stain positively
charged molecules
and structures,
such as proteins | Can be either a positive or negative stain, depending on the cell's chemistry. | | |\n| Negative
stains | India ink,
nigrosin | Stains background, not specimen | Dark background
with light specimen | 1 | | \n**Figure 2.40** (credit \"basic stains\": modification of work by Centers for Disease Control and Prevention; credit \"Acidic stains\": modification of work by Roberto Danovaro, Antonio Dell'Anno, Antonio Pusceddu, Cristina Gambi, Iben Heiner, Reinhardt Mobjerg Kristensen; credit \"Negative stains\": modification of work by Anh-Hue Tu) \n| | DIFFERENTIAL STAINS | | | | |\n|--------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------|-----------------------------------------|--|\n| Stain Type | Specific Dyes | Purpose | Outcome | Sample Images | |\n| Gram
stain | Uses crystal violet,
Gram's iodine,
ethanol
(decolorizer), and
safranin | Used to distinguish
cells by cell-wall
type (gram-positive,
gram-negative) | Gram-positive
cells stain
purple/violet.
Gram-negative
cells stain pink. | | |\n| Acid-fast
stain | After staining with basic fuchsin, acid-fast bacteria resist decolorization by acid-alcohol. Non acid-fast bacteria are counterstained with methylene blue. | Used to distinguish acid-fast bacteria such as M. tuberculosis , from non–acid-fast cells | Acid-fast
bacteria are red;
non–acid-fast
cells are blue. | ASM Workshitzeryong & Ziramennan | |\n| Endospore
stain | Uses heat to stain endospores with malachite green (Schaeffer-Fulton procedure), then cell is washed and counterstained with safranin. | Used to distinguish organisms with endospores from those without; used to study the endospore. | Endospores
appear
bluish-green;
other structures
appear pink to
red. | | |\n| Flagella
stain | Flagella are coated with a tannic acid or potassium alum mordant, then stained using either pararosaline or basic fuchsin. | Used to view and study flagella in bacteria that have them. | Flagella are
visible if present. | | |\n| Capsule
stain | Negative staining with India ink or nigrosin is used to stain the background, leaving a clear area of the cell and the capsule. Counterstaining can be used to stain the cell while leaving the capsule clear. | Used to distinguish cells with capsules from those without. | Capsules
appear clear or
as halos if
present. | ASM, MicrobioLibrary, org © Pfizer Inc. | | \n**Figure 2.41** (credit \"Gram stain\": modification of work by Nina Parker; credit \"Acid-fast stain\": modification of work by American Society for Microbiology; credit \"Endospore stain\": modification of work by American Society for Microbiology; credit \"Capsule stain\" : modification of work by American Society for Microbiology; credit \"Flagella stain\": modification of work by Centers for Disease Control and Prevention)\n\nSamples to be analyzed using a TEM must have very thin sections. But cells are too soft to cut thinly, even with diamond knives. To cut cells without damage, the cells must be embedded in plastic resin and then dehydrated through a series of soaks in ethanol solutions (50%, 60%, 70%, and so on). The ethanol replaces the water in the cells, and the resin dissolves in ethanol and enters the cell, where it solidifies. Next, **thin sections** are cut using a specialized device called an **ultramicrotome** (**[Figure 2.42](#page-90-0)**). Finally, samples are fixed to fine copper wire or carbon-fiber grids and stained—not with colored dyes, but with substances like uranyl acetate or osmium tetroxide, which contain electrondense heavy metal atoms. \n \n \n**Figure 2.42** (a) An ultramicrotome used to prepare specimens for a TEM. (b) A technician uses an ultramicrotome to slice a specimen into thin sections. (credit a: modification of work by \"Frost Museum\"/Flickr; credit b: modification of work by U.S. Fish and Wildlife Service Northeast Region) \nWhen samples are prepared for viewing using an SEM, they must also be dehydrated using an ethanol series. However, they must be even drier than is necessary for a TEM. Critical point drying with inert liquid carbon dioxide under pressure is used to displace the water from the specimen. After drying, the specimens are sputter-coated with metal by knocking atoms off of a palladium target, with energetic particles. Sputter-coating prevents specimens from becoming charged by the SEM's electron beam. \n \n- Why is it important to dehydrate cells before examining them under an electron microscope?\n- Name the device that is used to create thin sections of specimens for electron microscopy. \n#### **Micro Connections** \n#### **Using Microscopy to Diagnose Syphilis** \nThe causative agent of syphilis is *Treponema pallidum*, a flexible, spiral cell (spirochete) that can be very thin (<0.15 μm) and match the refractive index of the medium, making it difficult to view using brightfield microscopy. Additionally, this species has not been successfully cultured in the laboratory on an artificial medium; therefore, diagnosis depends upon successful identification using microscopic techniques and serology (analysis of body fluids, often looking for antibodies to a pathogen). Since fixation and staining would kill the cells, darkfield microscopy is typically used for observing live specimens and viewing their movements. However, other approaches can also be used. For example, the cells can be thickened with silver particles (in tissue sections) and observed using a light microscope. It is also possible to use fluorescence or electron microscopy to view *Treponema* (**[Figure 2.43](#page-91-0)**). \n \n**Figure 2.43** (a) Living, unstained *Treponema pallidum* spirochetes can be viewed under a darkfield microscope. (b) In this brightfield image, a modified Steiner silver stain is used to visualized *T. pallidum* spirochetes. Though the stain kills the cells, it increases the contrast to make them more visible. (c) While not used for standard diagnostic testing, *T. pallidum* can also be examined using scanning electron microscopy. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by Centers for Disease Control and Prevention) \nIn clinical settings, indirect immunofluorescence is often used to identify *Treponema.* A primary, unstained antibody attaches directly to the pathogen surface, and secondary antibodies \"tagged\" with a fluorescent stain attach to the primary antibody. Multiple secondary antibodies can attach to each primary antibody, amplifying the amount of stain attached to each *Treponema* cell, making them easier to spot (**[Figure 2.44](#page-91-1)**). \n \n**Figure 2.44** Indirect immunofluorescence can be used to identify *T. pallidum*, the causative agent of syphilis, in a specimen.\n\nSamples for fluorescence and confocal microscopy are prepared similarly to samples for light microscopy, except that the dyes are fluorochromes. Stains are often diluted in liquid before applying to the slide. Some dyes attach to an antibody to stain specific proteins on specific types of cells (immunofluorescence); others may attach to DNA molecules in a process called fluorescence in situ hybridization (FISH), causing cells to be stained based on whether they have a specific DNA sequence. \nSample preparation for two-photon microscopy is similar to fluorescence microscopy, except for the use of infrared dyes. Specimens for STM need to be on a very clean and atomically smooth surface. They are often mica coated with Au(111). Toluene vapor is a common fixative. \n \n• What is the main difference between preparing a sample for fluorescence microscopy versus light microscopy? \n#### **Link to Learning** \n \nCornell University's **[Case Studies in Microscopy \\(https://www.openstax.org/](https://www.openstax.org/l/22cornellstud) [l/22cornellstud\\)](https://www.openstax.org/l/22cornellstud)** offers a series of clinical problems based on real-life events. Each case study walks you through a clinical problem using appropriate techniques in microscopy at each step. \n#### **Clinical Focus** \n#### **Resolution** \nFrom the results of the Gram stain, the technician now knows that Cindy's infection is caused by spherical, gram-positive bacteria that form grape-like clusters, which is typical of staphylococcal bacteria. After some additional testing, the technician determines that these bacteria are the medically important species known as *Staphylococcus aureus*, a common culprit in wound infections. Because some strains of *S. aureus* are resistant to many antibiotics, skin infections may spread to other areas of the body and become serious, sometimes even resulting in amputations or death if the correct antibiotics are not used. \nAfter testing several antibiotics, the lab is able to identify one that is effective against this particular strain of *S. aureus*. Cindy's doctor quickly prescribes the medication and emphasizes the importance of taking the entire course of antibiotics, even if the infection appears to clear up before the last scheduled dose. This reduces the risk that any especially resistant bacteria could survive, causing a second infection or spreading to another person. \n*Go back to the [previous](#page-84-0) Clinical Focus box.* \n#### **Eye on Ethics** \n \n#### **Microscopy and Antibiotic Resistance** \nAs the use of antibiotics has proliferated in medicine, as well as agriculture, microbes have evolved to become more resistant. Strains of bacteria such as methicillin-resistant *S. aureus* (MRSA), which has developed a high level of resistance to many antibiotics, are an increasingly worrying problem, so much so that research is underway to develop new and more diversified antibiotics. \nFluorescence microscopy can be useful in testing the effectiveness of new antibiotics against resistant strains like MRSA. In a test of one new antibiotic derived from a marine bacterium, MC21-A (bromophene), researchers used the fluorescent dye SYTOX Green to stain samples of MRSA. SYTOX Green is often used to distinguish dead cells from living cells, with fluorescence microscopy. Live cells will not absorb the dye, but cells killed by an antibiotic will absorb the dye, since the antibiotic has damaged the bacterial cell membrane. In this particular case, MRSA bacteria that had been exposed to MC21-A did, indeed, appear green under the fluorescence microscope, leading researchers to conclude that it is an effective antibiotic against MRSA. \nOf course, some argue that developing new antibiotics will only lead to even more antibiotic-resistant microbes, so-called superbugs that could spawn epidemics before new treatments can be developed. For this reason, many health professionals are beginning to exercise more discretion in prescribing antibiotics. Whereas antibiotics were once routinely prescribed for common illnesses without a definite diagnosis, doctors and hospitals are much more likely to conduct additional testing to determine whether an antibiotic is necessary and appropriate before prescribing. \nA sick patient might reasonably object to this stingy approach to prescribing antibiotics. To the patient who simply wants to feel better as quickly as possible, the potential benefits of taking an antibiotic may seem to outweigh any immediate health risks that might occur if the antibiotic is ineffective. But at what point do the risks of widespread antibiotic use supersede the desire to use them in individual cases?",
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"Header 1": "**How We See the Invisible World**",
"Header 2": "Staining Microscopic Specimens",
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"page_content": "#### **[2.1 The Properties of Light](#page-53-0)** \n- Light waves interacting with materials may be **reflected**, **absorbed**, or **transmitted**, depending on the properties of the material.\n- Light waves can interact with each other (**interference**) or be distorted by interactions with small objects or openings (**diffraction**).\n- **Refraction** occurs when light waves change speed and direction as they pass from one medium to another. Differences in the **refraction indices** of two materials determine the magnitude of directional changes when light passes from one to the other.\n- A **lens** is a medium with a curved surface that refracts and focuses light to produce an image.\n- Visible light is part of the **electromagnetic spectrum**; light waves of different frequencies and wavelengths are distinguished as colors by the human eye.\n- A prism can separate the colors of white light (**dispersion**) because different frequencies of light have different refractive indices for a given material.\n- **Fluorescent dyes** and **phosphorescent** materials can effectively transform nonvisible electromagnetic radiation into visible light.\n- The power of a microscope can be described in terms of its **magnification** and **resolution**.\n- Resolution can be increased by shortening wavelength, increasing the **numerical aperture** of the lens, or using stains that enhance contrast. \n#### **[2.2 Peering Into the Invisible World](#page-59-0)** \n- **Antonie van Leeuwenhoek** is credited with the first observation of microbes, including protists and bacteria, with simple microscopes that he made.\n- **Robert Hooke** was the first to describe what we now call cells.\n- **Simple microscopes** have a single lens, while **compound microscopes** have multiple lenses. \n#### **[2.3 Instruments of Microscopy](#page-62-0)** \n- Numerous types of microscopes use various technologies to generate micrographs. Most are useful for a particular type of specimen or application.\n- **Light microscopy** uses lenses to focus light on a specimen to produce an image. Commonly used light microscopes include **brightfield**, **darkfield**, **phase-contrast**, **differential interference contrast**, \n**fluorescence**, **confocal**, and **two-photon** microscopes. \n- **Electron microscopy** focuses electrons on the specimen using magnets, producing much greater magnification than light microscopy. The **transmission electron microscope (TEM)** and **scanning electron microscope (SEM)** are two common forms.\n- **Scanning probe microscopy** produces images of even greater magnification by measuring feedback from sharp probes that interact with the specimen. Probe microscopes include the **scanning tunneling microscope (STM)** and the **atomic force microscope (AFM)**. \n#### **[2.4 Staining Microscopic Specimens](#page-80-0)** \n- Samples must be properly prepared for microscopy. This may involve **staining**, **fixation**, and/or cutting **thin sections**.\n- A variety of staining techniques can be used with light microscopy, including **Gram staining, acid-fast staining**, **capsule staining**, **endospore staining,** and **flagella staining**.\n- Samples for TEM require very thin sections, whereas samples for SEM require sputter-coating.\n- Preparation for fluorescence microscopy is similar to that for light microscopy, except that fluorochromes are used.\n\n#### **Multiple Choice** \n- **1.** Which of the following has the highest energy?\n- a. light with a long wavelength\n- b. light with an intermediate wavelength\n- c. light with a short wavelength\n- d. It is impossible to tell from the information given.\n- **2.** You place a specimen under the microscope and notice that parts of the specimen begin to emit light immediately. These materials can be described as\n- a. fluorescent \n\\_\\_\\_\\_\\_\\_\\_\\_\\_\\_\\_\\_\\_. \n- b. phosphorescent\n- c. transparent\n- d. opaque\n- **3.** Who was the first to describe \"cells\" in dead cork tissue?\n- a. Hans Janssen\n- b. Zaccharias Janssen\n- c. Antonie van Leeuwenhoek\n- d. Robert Hooke\n- **4.** Who is the probable inventor of the compound microscope?\n- a. Girolamo Fracastoro\n- b. Zaccharias Janssen\n- c. Antonie van Leeuwenhoek\n- d. Robert Hooke \n- **5.** Which would be the best choice for viewing internal structures of a living protist such as a *Paramecium*?\n- a. a brightfield microscope with a stain\n- b. a brightfield microscope without a stain\n- c. a darkfield microscope\n- d. a transmission electron microscope\n- **6.** Which type of microscope is especially useful for viewing thick structures such as biofilms?\n- a. a transmission electron microscope\n- b. a scanning electron microscopes\n- c. a phase-contrast microscope\n- d. a confocal scanning laser microscope\n- e. an atomic force microscope\n- **7.** Which type of microscope would be the best choice for viewing very small surface structures of a cell?\n- a. a transmission electron microscope\n- b. a scanning electron microscope\n- c. a brightfield microscope\n- d. a darkfield microscope\n- e. a phase-contrast microscope\n- **8.** What type of microscope uses an annular stop?\n- a. a transmission electron microscope\n- b. a scanning electron microscope\n- c. a brightfield microscope\n- d. a darkfield microscope\n- e. a phase-contrast microscope \n- **9.** What type of microscope uses a cone of light so that light only hits the specimen indirectly, producing a darker image on a brighter background?\n- a. a transmission electron microscope\n- b. a scanning electron microscope\n- c. a brightfield microscope\n- d. a darkfield microscope\n- e. a phase-contrast microscope\n- **10.** What mordant is used in Gram staining?\n- a. crystal violet\n- b. safranin\n- c. acid-alcohol\n- d. iodine\n- **11.** What is one difference between specimen preparation for a transmission electron microscope (TEM) and preparation for a scanning electron microscope (SEM)?\n- a. Only the TEM specimen requires sputter coating.\n- b. Only the SEM specimen requires sputtercoating.\n- c. Only the TEM specimen must be dehydrated.\n- d. Only the SEM specimen must be dehydrated. \n#### **Fill in the Blank** \n| 17.
18. | Ziehl-Neelsen staining, a type of staining, is diagnostic for
Mycobacterium tuberculosis.
The is used to differentiate bacterial cells based on the components of their cell walls. |\n|------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| 16. | What is the total magnification of a specimen that is being viewed with a standard ocular lens and a 40⨯
objective lens? |\n| 15. | In a(n) microscope, a probe located just above the specimen moves up and down in response to forces
between the atoms and the tip of the probe. |\n| 14. | Chromophores that absorb and then emit light are called |\n| 13. | A microscope that uses multiple lenses is called a microscope. |\n| 12. | When you see light bend as it moves from air into water, you are observing |\n| | | \n- **19.** Explain how a prism separates white light into different colors.\n- **20.** Why is Antonie van Leeuwenhoek's work much better known than that of Zaccharias Janssen?\n- **21.** Why did the cork cells observed by Robert Hooke appear to be empty, as opposed to being full of other structures?\n- **22.** What is the function of the condenser in a brightfield microscope? \n#### **Art Connection** \n**23.** Label each component of the brightfield microscope. \n \n**24.** How could you identify whether a particular bacterial sample contained specimens with mycolic acid-rich cell walls? \n#### **Critical Thinking** \n- **25.** In **[Figure 2.7](#page-57-0)**, which of the following has the lowest energy?\n- a. visible light\n- b. X-rays\n- c. ultraviolet rays\n- d. infrared rays\n- **26.** When focusing a light microscope, why is it best to adjust the focus using the coarse focusing knob before using the fine focusing knob?\n- **27.** You need to identify structures within a cell using a microscope. However, the image appears very blurry even though you have a high magnification. What are some things that you could try to improve the resolution of the image? Describe the most basic factors that affect resolution when you first put the slide onto the stage; then consider more specific factors that could affect resolution for 40⨯ and 100⨯ lenses.\n- **28.** You use the Gram staining procedure to stain an L-form bacterium (a bacterium that lacks a cell wall). What color will the bacterium be after the staining procedure is finished?",
"metadata": {
"Header 1": "**How We See the Invisible World**",
"Header 2": "Summary and Review Questions",
"is_merged_section": true,
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": " \n**Figure 3.1** Microorganisms vary visually in their size and shape, as can be observed microscopically; but they also vary in invisible ways, such as in their metabolic capabilities. (credit a, e, f: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by NIAID; credit c: modification of work by CSIRO; credit d: modification of work by \"Microscopic World\"/YouTube) \n#### **Chapter Outline** \n- [3.1 Spontaneous Generation](#page-99-0)\n- [3.2 Foundations of Modern Cell Theory](#page-103-0)\n- [3.3 Unique Characteristics of Prokaryotic Cells](#page-111-0)\n- [3.4 Unique Characteristics of Eukaryotic Cells](#page-131-0)",
"metadata": {
"Header 1": "**The Cell**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "Life takes many forms, from giant redwood trees towering hundreds of feet in the air to the tiniest known microbes, which measure only a few billionths of a meter. Humans have long pondered life's origins and debated the defining characteristics of life, but our understanding of these concepts has changed radically since the invention of the microscope. In the 17th century, observations of microscopic life led to the development of the cell theory: the idea that the fundamental unit of life is the cell, that all organisms contain at least one cell, and that cells only come from other cells. \nDespite sharing certain characteristics, cells may vary significantly. The two main types of cells are prokaryotic cells (lacking a nucleus) and eukaryotic cells (containing a well-organized, membrane-bound nucleus). Each type of cell exhibits remarkable variety in structure, function, and metabolic activity (**[Figure 3.1](#page-98-1)**). This chapter will focus on the historical discoveries that have shaped our current understanding of microbes, including their origins and their role in human disease. We will then explore the distinguishing structures found in prokaryotic and eukaryotic cells.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Introduction**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "#### **Learning Objectives** \n• Explain the theory of spontaneous generation and why people once accepted it as an explanation for the existence of certain types of organisms \n• Explain how certain individuals (van Helmont, Redi, Needham, Spallanzani, and Pasteur) tried to prove or disprove spontaneous generation \nHumans have been asking for millennia: Where does new life come from? Religion, philosophy, and science have all wrestled with this question. One of the oldest explanations was the theory of spontaneous generation, which can be traced back to the ancient Greeks and was widely accepted through the Middle Ages. \n#### **The Theory of Spontaneous Generation** \nThe Greek philosopher Aristotle (384–322 BC) was one of the earliest recorded scholars to articulate the theory of **spontaneous generation**, the notion that life can arise from nonliving matter. Aristotle proposed that life arose from nonliving material if the material contained *pneuma* (\"vital heat\"). As evidence, he noted several instances of the appearance of animals from environments previously devoid of such animals, such as the seemingly sudden appearance of fish in a new puddle of water.[1] \nThis theory persisted into the 17th century, when scientists undertook additional experimentation to support or disprove it. By this time, the proponents of the theory cited how frogs simply seem to appear along the muddy banks of the Nile River in Egypt during the annual flooding. Others observed that mice simply appeared among grain stored in barns with thatched roofs. When the roof leaked and the grain molded, mice appeared. Jan Baptista van Helmont, a 17th century Flemish scientist, proposed that mice could arise from rags and wheat kernels left in an open container for 3 weeks. In reality, such habitats provided ideal food sources and shelter for mouse populations to flourish. \nHowever, one of van Helmont's contemporaries, Italian physician Francesco Redi (1626–1697), performed an experiment in 1668 that was one of the first to refute the idea that maggots (the larvae of flies) spontaneously generate on meat left out in the open air. He predicted that preventing flies from having direct contact with the meat would also prevent the appearance of maggots. Redi left meat in each of six containers (**[Figure 3.2](#page-100-0)**). Two were open to the air, two were covered with gauze, and two were tightly sealed. His hypothesis was supported when maggots developed in the uncovered jars, but no maggots appeared in either the gauze-covered or the tightly sealed jars. He concluded that maggots could only form when flies were allowed to lay eggs in the meat, and that the maggots were the offspring of flies, not the product of spontaneous generation. \n#### **Clinical Focus** \n#### **Part 1** \nBarbara is a 19-year-old college student living in the dormitory. In January, she came down with a sore throat, headache, mild fever, chills, and a violent but unproductive (i.e., no mucus) cough. To treat these symptoms, Barbara began taking an over-the-counter cold medication, which did not seem to work. In fact, over the next few days, while some of Barbara's symptoms began to resolve, her cough and fever persisted, and she felt very tired and weak. \n• What types of respiratory disease may be responsible? \n*Jump to the [next](#page-109-0) Clinical Focus box* \n1. K. Zwier. \"Aristotle on Spontaneous Generation.\" http://www.sju.edu/int/academics/cas/resources/gppc/pdf/Karen%20R.%20Zwier.pdf \n \n**Figure 3.2** Francesco Redi's experimental setup consisted of an open container, a container sealed with a cork top, and a container covered in mesh that let in air but not flies. Maggots only appeared on the meat in the open container. However, maggots were also found on the gauze of the gauze-covered container. \nIn 1745, John Needham (1713–1781) published a report of his own experiments, in which he briefly boiled broth infused with plant or animal matter, hoping to kill all preexisting microbes.[2] He then sealed the flasks. After a few days, Needham observed that the broth had become cloudy and a single drop contained numerous microscopic creatures. He argued that the new microbes must have arisen spontaneously. In reality, however, he likely did not boil the broth enough to kill all preexisting microbes. \nLazzaro Spallanzani (1729–1799) did not agree with Needham's conclusions, however, and performed hundreds of carefully executed experiments using heated broth.[3] As in Needham's experiment, broth in sealed jars and unsealed jars was infused with plant and animal matter. Spallanzani's results contradicted the findings of Needham: Heated but sealed flasks remained clear, without any signs of spontaneous growth, unless the flasks were subsequently opened to the air. This suggested that microbes were introduced into these flasks from the air. In response to Spallanzani's findings, Needham argued that life originates from a \"life force\" that was destroyed during Spallanzani's extended boiling. Any subsequent sealing of the flasks then prevented new life force from entering and causing spontaneous generation (**[Figure 3.3](#page-101-0)**). \n2. E. Capanna. \"Lazzaro Spallanzani: At the Roots of Modern Biology.\" *Journal of Experimental Zoology* 285 no. 3 (1999):178–196. \n3. R. Mancini, M. Nigro, G. Ippolito. \"Lazzaro Spallanzani and His Refutation of the Theory of Spontaneous Generation.\" *Le Infezioni in Medicina* 15 no. 3 (2007):199–206. \n \n \n \n**Figure 3.3** (a) Francesco Redi, who demonstrated that maggots were the offspring of flies, not products of spontaneous generation. (b) John Needham, who argued that microbes arose spontaneously in broth from a \"life force.\" (c) Lazzaro Spallanzani, whose experiments with broth aimed to disprove those of Needham. \n \n- Describe the theory of spontaneous generation and some of the arguments used to support it.\n- Explain how the experiments of Redi and Spallanzani challenged the theory of spontaneous generation.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**3.1 Spontaneous Generation**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "The debate over spontaneous generation continued well into the 19th century, with scientists serving as proponents of both sides. To settle the debate, the Paris Academy of Sciences offered a prize for resolution of the problem. Louis Pasteur, a prominent French chemist who had been studying microbial fermentation and the causes of wine spoilage, accepted the challenge. In 1858, Pasteur filtered air through a gun-cotton filter and, upon microscopic examination of the cotton, found it full of microorganisms, suggesting that the exposure of a broth to air was not introducing a \"life force\" to the broth but rather airborne microorganisms. \nLater, Pasteur made a series of flasks with long, twisted necks (\"swan-neck\" flasks), in which he boiled broth to sterilize it (**[Figure 3.4](#page-102-0)**). His design allowed air inside the flasks to be exchanged with air from the outside, but prevented the introduction of any airborne microorganisms, which would get caught in the twists and bends of the flasks' necks. If a life force besides the airborne microorganisms were responsible for microbial growth within the sterilized flasks, it would have access to the broth, whereas the microorganisms would not. He correctly predicted that sterilized broth in his swan-neck flasks would remain sterile as long as the swan necks remained intact. However, should the necks be broken, microorganisms would be introduced, contaminating the flasks and allowing microbial growth within the broth. \nPasteur's set of experiments irrefutably disproved the theory of spontaneous generation and earned him the prestigious Alhumbert Prize from the Paris Academy of Sciences in 1862. In a subsequent lecture in 1864, Pasteur articulated \"*Omne vivum ex vivo*\" (\"Life only comes from life\"). In this lecture, Pasteur recounted his famous swanneck flask experiment, stating that \"…life is a germ and a germ is life. Never will the doctrine of spontaneous generation recover from the mortal blow of this simple experiment.\"[4] To Pasteur's credit, it never has. \n4. R. Vallery-Radot. *The Life of Pasteur*, trans. R.L. Devonshire. New York: McClure, Phillips and Co, 1902, 1:142. \n \n**Figure 3.4** (a) French scientist Louis Pasteur, who definitively refuted the long-disputed theory of spontaneous generation. (b) The unique swan-neck feature of the flasks used in Pasteur's experiment allowed air to enter the flask but prevented the entry of bacterial and fungal spores. (c) Pasteur's experiment consisted of two parts. In the first part, the broth in the flask was boiled to sterilize it. When this broth was cooled, it remained free of contamination. In the second part of the experiment, the flask was boiled and then the neck was broken off. The broth in this flask became contaminated. (credit b: modification of work by \"Wellcome Images\"/Wikimedia Commons) \n \n- How did Pasteur's experimental design allow air, but not microbes, to enter, and why was this important?\n- What was the control group in Pasteur's experiment and what did it show?",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**3.1 Spontaneous Generation**",
"Header 3": "**Disproving Spontaneous Generation**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "#### **Learning Objectives** \n- Explain the key points of cell theory and the individual contributions of Hooke, Schleiden, Schwann, Remak, and Virchow\n- Explain the key points of endosymbiotic theory and cite the evidence that supports this concept\n- Explain the contributions of Semmelweis, Snow, Pasteur, Lister, and Koch to the development of germ theory \nWhile some scientists were arguing over the theory of spontaneous generation, other scientists were making discoveries leading to a better understanding of what we now call the cell theory. Modern cell theory has two basic tenets: \n- All cells only come from other cells (the principle of biogenesis).\n- Cells are the fundamental units of organisms. \nToday, these tenets are fundamental to our understanding of life on earth. However, modern cell theory grew out of the collective work of many scientists.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**3.2 Foundations of Modern Cell Theory**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "The English scientist Robert Hooke first used the term \"cells\" in 1665 to describe the small chambers within cork that he observed under a microscope of his own design. To Hooke, thin sections of cork resembled \"Honey-comb,\" or \"small Boxes or Bladders of Air.\" He noted that each \"Cavern, Bubble, or Cell\" was distinct from the others (**[Figure](#page-103-1) [3.5](#page-103-1)**). At the time, Hooke was not aware that the cork cells were long dead and, therefore, lacked the internal structures found within living cells. \n \n**Figure 3.5** Robert Hooke (1635–1703) was the first to describe cells based upon his microscopic observations of cork. This illustration was published in his work *Micrographia*. \nDespite Hooke's early description of cells, their significance as the fundamental unit of life was not yet recognized. Nearly 200 years later, in 1838, Matthias Schleiden (1804–1881), a German botanist who made extensive microscopic observations of plant tissues, described them as being composed of cells. Visualizing plant cells was relatively easy because plant cells are clearly separated by their thick cell walls. Schleiden believed that cells formed through crystallization, rather than cell division. \nTheodor Schwann (1810–1882), a noted German physiologist, made similar microscopic observations of animal tissue. In 1839, after a conversation with Schleiden, Schwann realized that similarities existed between plant and \nanimal tissues. This laid the foundation for the idea that cells are the fundamental components of plants and animals. \nIn the 1850s, two Polish scientists living in Germany pushed this idea further, culminating in what we recognize today as the modern cell theory. In 1852, Robert Remak (1815–1865), a prominent neurologist and embryologist, published convincing evidence that cells are derived from other cells as a result of cell division. However, this idea was questioned by many in the scientific community. Three years later, Rudolf Virchow (1821–1902), a wellrespected pathologist, published an editorial essay entitled \"Cellular Pathology,\" which popularized the concept of cell theory using the Latin phrase *omnis cellula a cellula* (\"all cells arise from cells\"), which is essentially the second tenet of modern cell theory.[5] Given the similarity of Virchow's work to Remak's, there is some controversy as to which scientist should receive credit for articulating cell theory. See the following Eye on Ethics feature for more about this controversy. \n#### **Eye on Ethics** \n \n#### **Science and Plagiarism** \nRudolf Virchow, a prominent, Polish-born, German scientist, is often remembered as the \"Father of Pathology.\" Well known for innovative approaches, he was one of the first to determine the causes of various diseases by examining their effects on tissues and organs. He was also among the first to use animals in his research and, as a result of his work, he was the first to name numerous diseases and created many other medical terms. Over the course of his career, he published more than 2,000 papers and headed various important medical facilities, including the Charité – Universitätsmedizin Berlin, a prominent Berlin hospital and medical school. But he is, perhaps, best remembered for his 1855 editorial essay titled \"Cellular Pathology,\" published in *Archiv für Pathologische Anatomie und Physiologie*, a journal that Virchow himself cofounded and still exists today. \nDespite his significant scientific legacy, there is some controversy regarding this essay, in which Virchow proposed the central tenet of modern cell theory—that all cells arise from other cells. Robert Remak, a former colleague who worked in the same laboratory as Virchow at the University of Berlin, had published the same idea 3 years before. Though it appears Virchow was familiar with Remak's work, he neglected to credit Remak's ideas in his essay. When Remak wrote a letter to Virchow pointing out similarities between Virchow's ideas and his own, Virchow was dismissive. In 1858, in the preface to one of his books, Virchow wrote that his 1855 publication was just an editorial piece, not a scientific paper, and thus there was no need to cite Remak's work. \nBy today's standards, Virchow's editorial piece would certainly be considered an act of plagiarism, since he presented Remak's ideas as his own. However, in the 19th century, standards for academic integrity were much less clear. Virchow's strong reputation, coupled with the fact that Remak was a Jew in a somewhat anti-Semitic political climate, shielded him from any significant repercussions. Today, the process of peer review and the ease of access to the scientific literature help discourage plagiarism. Although scientists are still motivated to publish original ideas that advance scientific knowledge, those who would consider plagiarizing are well aware of the serious consequences. \nIn academia, plagiarism represents the theft of both individual thought and research—an offense that can destroy reputations and end careers.[6] [7] [8] [9] \n- 5. M. Schultz. \"Rudolph Virchow.\" *Emerging Infectious Diseases* 14 no. 9 (2008):1480–1481.\n- 6. B. Kisch. \"Forgotten Leaders in Modern Medicine, Valentin, Gouby, Remak, Auerbach.\" *Transactions of the American Philosophical Society* 44 (1954):139–317.\n- 7. H. Harris. *The Birth of the Cell*. New Haven, CT: Yale University Press, 2000:133.\n- 8. C. Webster (ed.). *Biology, Medicine and Society 1840-1940*. Cambridge, UK; Cambridge University Press, 1981:118–119.\n- 9. C. Zuchora-Walske. *Key Discoveries in Life Science*. Minneapolis, MN: Lerner Publishing, 2015:12–13. \n \n \n**Figure 3.6** (a) Rudolf Virchow (1821–1902) popularized the cell theory in an 1855 essay entitled \"Cellular Pathology*.\"* (b) The idea that all cells originate from other cells was first published in 1852 by his contemporary and former colleague Robert Remak (1815–1865). \n \n- What are the key points of the cell theory?\n- What contributions did Rudolf Virchow and Robert Remak make to the development of the cell theory?",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**3.2 Foundations of Modern Cell Theory**",
"Header 3": "**The Origins of Cell Theory**",
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"page_content": "As scientists were making progress toward understanding the role of cells in plant and animal tissues, others were examining the structures within the cells themselves. In 1831, Scottish botanist Robert Brown (1773–1858) was the first to describe observations of nuclei, which he observed in plant cells. Then, in the early 1880s, German botanist Andreas Schimper (1856–1901) was the first to describe the chloroplasts of plant cells, identifying their role in starch formation during photosynthesis and noting that they divided independent of the nucleus. \nBased upon the chloroplasts' ability to reproduce independently, Russian botanist Konstantin Mereschkowski (1855–1921) suggested in 1905 that chloroplasts may have originated from ancestral photosynthetic bacteria living symbiotically inside a eukaryotic cell. He proposed a similar origin for the nucleus of plant cells. This was the first articulation of the endosymbiotic hypothesis, and would explain how eukaryotic cells evolved from ancestral bacteria. \nMereschkowski's endosymbiotic hypothesis was furthered by American anatomist Ivan Wallin (1883–1969), who began to experimentally examine the similarities between mitochondria, chloroplasts, and bacteria—in other words, to put the endosymbiotic hypothesis to the test using objective investigation. Wallin published a series of papers in the 1920s supporting the endosymbiotic hypothesis, including a 1926 publication co-authored with Mereschkowski. Wallin claimed he could culture mitochondria outside of their eukaryotic host cells. Many scientists dismissed his cultures of mitochondria as resulting from bacterial contamination. Modern genome sequencing work supports the dissenting scientists by showing that much of the genome of mitochondria had been transferred to the host cell's nucleus, preventing the mitochondria from being able to live on their own.[10] [11] \n10. T. Embley, W. Martin. \"Eukaryotic Evolution, Changes, and Challenges.\" *Nature* Vol. 440 (2006):623–630. \nWallin's ideas regarding the endosymbiotic hypothesis were largely ignored for the next 50 years because scientists were unaware that these organelles contained their own DNA. However, with the discovery of mitochondrial and chloroplast DNA in the 1960s, the endosymbiotic hypothesis was resurrected. Lynn Margulis (1938–2011), an American geneticist, published her ideas regarding the endosymbiotic hypothesis of the origins of mitochondria and chloroplasts in 1967.[12] In the decade leading up to her publication, advances in microscopy had allowed scientists to differentiate prokaryotic cells from eukaryotic cells. In her publication, Margulis reviewed the literature and argued that the eukaryotic organelles such as mitochondria and chloroplasts are of prokaryotic origin. She presented a growing body of microscopic, genetic, molecular biology, fossil, and geological data to support her claims. \nAgain, this hypothesis was not initially popular, but mounting genetic evidence due to the advent of DNA sequencing supported the **endosymbiotic theory**, which is now defined as the theory that mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host (**[Figure 3.7](#page-107-0)**). With Margulis' initial endosymbiotic theory gaining wide acceptance, she expanded on the theory in her 1981 book *Symbiosis in Cell Evolution*. In it, she explains how endosymbiosis is a major driving factor in the evolution of organisms. More recent genetic sequencing and phylogenetic analysis show that mitochondrial DNA and chloroplast DNA are highly related to their bacterial counterparts, both in DNA sequence and chromosome structure. However, mitochondrial DNA and chloroplast DNA are reduced compared with nuclear DNA because many of the genes have moved from the organelles into the host cell's nucleus. Additionally, mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, rather than to the eukaryotic ribosomes of their hosts. Last, the binary fission of these organelles strongly resembles the binary fission of bacteria, as compared with mitosis performed by eukaryotic cells. Since Margulis' original proposal, scientists have observed several examples of bacterial endosymbionts in modern-day eukaryotic cells. Examples include the endosymbiotic bacteria found within the guts of certain insects, such as cockroaches,[13] and photosynthetic bacteria-like organelles found in protists.[14] \n11. O.G. Berg, C.G. Kurland. \"Why Mitochondrial Genes Are Most Often Found in Nuclei.\" *Molecular Biology and Evolution* 17 no. 6 (2000):951–961. \n12. L. *Sagan. \"On the Origin of Mitosing Cells.\" Journal of Theoretical Biology 14 no. 3 (1967):225–274.* \n13. A.E. Douglas. \"The Microbial Dimension in Insect Nutritional Ecology.\" *Functional Ecology* 23 (2009):38–47. \n14. J.M. Jaynes, L.P. Vernon. \"The Cyanelle of *Cyanophora paradoxa*: Almost a Cyanobacterial Chloroplast.\" *Trends in Biochemical Sciences* 7 no. 1 (1982):22–24. \n**Figure 3.7** According to the endosymbiotic theory, mitochondria and chloroplasts are each derived from the uptake of bacteria. These bacteria established a symbiotic relationship with their host cell that eventually led to the bacteria evolving into mitochondria and chloroplasts. \n \n- What does the modern endosymbiotic theory state?\n- What evidence supports the endosymbiotic theory?",
"metadata": {
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"Header 2": "**3.2 Foundations of Modern Cell Theory**",
"Header 3": "**Endosymbiotic Theory**",
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"page_content": "Prior to the discovery of microbes during the 17th century, other theories circulated about the origins of disease. For example, the ancient Greeks proposed the miasma theory, which held that disease originated from particles emanating from decomposing matter, such as that in sewage or cesspits. Such particles infected humans in close proximity to the rotting material. Diseases including the Black Death, which ravaged Europe's population during the Middle Ages, were thought to have originated in this way. \nIn 1546, Italian physician Girolamo Fracastoro proposed, in his essay *De Contagione et Contagiosis Morbis*, that seed-like spores may be transferred between individuals through direct contact, exposure to contaminated clothing, or through the air. We now recognize Fracastoro as an early proponent of the **germ theory of disease**, which states that diseases may result from microbial infection. However, in the 16th century, Fracastoro's ideas were not widely accepted and would be largely forgotten until the 19th century. \nIn 1847, Hungarian obstetrician Ignaz Semmelweis (**[Figure 3.8](#page-108-0)**) observed that mothers who gave birth in hospital wards staffed by physicians and medical students were more likely to suffer and die from puerperal fever after childbirth (10%–20% mortality rate) than were mothers in wards staffed by midwives (1% mortality rate). Semmelweis observed medical students performing autopsies and then subsequently carrying out vaginal examinations on living patients without washing their hands in between. He suspected that the students carried disease \nfrom the autopsies to the patients they examined. His suspicions were supported by the untimely death of a friend, a physician who contracted a fatal wound infection after a postmortem examination of a woman who had died of a puerperal infection. The dead physician's wound had been caused by a scalpel used during the examination, and his subsequent illness and death closely paralleled that of the dead patient. \nAlthough Semmelweis did not know the true cause of puerperal fever, he proposed that physicians were somehow transferring the causative agent to their patients. He suggested that the number of puerperal fever cases could be reduced if physicians and medical students simply washed their hands with chlorinated lime water before and after examining every patient. When this practice was implemented, the maternal mortality rate in mothers cared for by physicians dropped to the same 1% mortality rate observed among mothers cared for by midwives. This demonstrated that handwashing was a very effective method for preventing disease transmission. Despite this great success, many discounted Semmelweis's work at the time, and physicians were slow to adopt the simple procedure of handwashing to prevent infections in their patients because it contradicted established norms for that time period. \n \n**Figure 3.8** Ignaz Semmelweis (1818–1865) was a proponent of the importance of handwashing to prevent transfer of disease between patients by physicians. \nAround the same time Semmelweis was promoting handwashing, in 1848, British physician John Snow conducted studies to track the source of cholera outbreaks in London. By tracing the outbreaks to two specific water sources, both of which were contaminated by sewage, Snow ultimately demonstrated that cholera bacteria were transmitted via drinking water. Snow's work is influential in that it represents the first known epidemiological study, and it resulted in the first known public health response to an epidemic. The work of both Semmelweis and Snow clearly refuted the prevailing miasma theory of the day, showing that disease is not only transmitted through the air but also through contaminated items. \nAlthough the work of Semmelweis and Snow successfully showed the role of sanitation in preventing infectious disease, the cause of disease was not fully understood. The subsequent work of Louis Pasteur, Robert Koch, and Joseph Lister would further substantiate the germ theory of disease. \nWhile studying the causes of beer and wine spoilage in 1856, Pasteur discovered properties of fermentation by microorganisms. He had demonstrated with his swan-neck flask experiments (**[Figure 3.4](#page-102-0)**) that airborne microbes, not spontaneous generation, were the cause of food spoilage, and he suggested that if microbes were responsible for food spoilage and fermentation, they could also be responsible for causing infection. This was the foundation for the germ theory of disease. \nMeanwhile, British surgeon Joseph Lister (**[Figure 3.9](#page-109-1)**) was trying to determine the causes of postsurgical infections. Many physicians did not give credence to the idea that microbes on their hands, on their clothes, or in the air could infect patients' surgical wounds, despite the fact that 50% of surgical patients, on average, were dying of postsurgical infections.[15] Lister, however, was familiar with the work of Semmelweis and Pasteur; therefore, he insisted on \nhandwashing and extreme cleanliness during surgery. In 1867, to further decrease the incidence of postsurgical wound infections, Lister began using carbolic acid (phenol) spray disinfectant/antiseptic during surgery. His extremely successful efforts to reduce postsurgical infection caused his techniques to become a standard medical practice. \nA few years later, Robert Koch (**[Figure 3.9](#page-109-1)**) proposed a series of postulates (Koch's postulates) based on the idea that the cause of a specific disease could be attributed to a specific microbe. Using these postulates, Koch and his colleagues were able to definitively identify the causative pathogens of specific diseases, including anthrax, tuberculosis, and cholera. Koch's \"one microbe, one disease\" concept was the culmination of the 19th century's paradigm shift away from miasma theory and toward the germ theory of disease. Koch's postulates are discussed more thoroughly in **[How Pathogens Cause Disease](#page-674-0)**. \n \n \n**Figure 3.9** (a) Joseph Lister developed procedures for the proper care of surgical wounds and the sterilization of surgical equipment. (b) Robert Koch established a protocol to determine the cause of infectious disease. Both scientists contributed significantly to the acceptance of the germ theory of disease. \n \n- Compare and contrast the miasma theory of disease with the germ theory of disease.\n- How did Joseph Lister's work contribute to the debate between the miasma theory and germ theory and how did this increase the success of medical procedures? \n#### **Clinical Focus** \n#### **Part 2** \nAfter suffering a fever, congestion, cough, and increasing aches and pains for several days, Barbara suspects that she has a case of the flu. She decides to visit the health center at her university. The PA tells Barbara that her symptoms could be due to a range of diseases, such as influenza, bronchitis, pneumonia, or tuberculosis. \nDuring her physical examination, the PA notes that Barbara's heart rate is slightly elevated. Using a pulse oximeter, a small device that clips on her finger, he finds that Barbara has hypoxemia—a lower-than-normal level of oxygen in the blood. Using a stethoscope, the PA listens for abnormal sounds made by Barbara's heart, lungs, and digestive system. As Barbara breathes, the PA hears a crackling sound and notes a slight shortness of breath. He collects a sputum sample, noting the greenish color of the mucus, and orders a chest radiograph, which shows a \"shadow\" in the left lung. All of these signs are suggestive of pneumonia, a condition in which \nthe lungs fill with mucus (**[Figure 3.10](#page-110-0)**). \n \n \n \n**Figure 3.10** This is a chest radiograph typical of pneumonia. Because X-ray images are negative images, a \"shadow\" is seen as a white area within the lung that should otherwise be black. In this case, the left lung shows a shadow as a result of pockets in the lung that have become filled with fluid. (credit left: modification of work by \"Christaras A\"/Wikimedia Commons) \n• What kinds of infectious agents are known to cause pneumonia? \n*Jump to the [next](#page-127-0) Clinical Focus box. Go back to the [previous](#page-99-1) Clinical Focus box.* \n \n**Figure 3.11** (credit \"swan-neck flask\": modification of work by Wellcome Images)",
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"Header 2": "**The Germ Theory of Disease**",
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"page_content": "#### **Learning Objectives** \n- Explain the distinguishing characteristics of prokaryotic cells\n- Describe common cell morphologies and cellular arrangements typical of prokaryotic cells and explain how cells maintain their morphology\n- Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function\n- Compare the distinguishing characteristics of bacterial and archaeal cells \nCell theory states that the cell is the fundamental unit of life. However, cells vary significantly in size, shape, structure, and function. At the simplest level of construction, all cells possess a few fundamental components. These include **cytoplasm** (a gel-like substance composed of water and dissolved chemicals needed for growth), which is contained within a plasma membrane (also called a cell membrane or cytoplasmic membrane); one or more chromosomes, which contain the genetic blueprints of the cell; and **ribosomes**, organelles used for the production of proteins. \nBeyond these basic components, cells can vary greatly between organisms, and even within the same multicellular organism. The two largest categories of cells—**prokaryotic cells** and **eukaryotic cells**—are defined by major differences in several cell structures. Prokaryotic cells lack a nucleus surrounded by a complex nuclear membrane \nand generally have a single, circular chromosome located in a nucleoid. Eukaryotic cells have a nucleus surrounded by a complex nuclear membrane that contains multiple, rod-shaped chromosomes.[16] \nAll plant cells and animal cells are eukaryotic. Some microorganisms are composed of prokaryotic cells, whereas others are composed of eukaryotic cells. Prokaryotic microorganisms are classified within the domains Archaea and Bacteria, whereas eukaryotic organisms are classified within the domain Eukarya. \nThe structures inside a cell are analogous to the organs inside a human body, with unique structures suited to specific functions. Some of the structures found in prokaryotic cells are similar to those found in some eukaryotic cells; others are unique to prokaryotes. Although there are some exceptions, eukaryotic cells tend to be larger than prokaryotic cells. The comparatively larger size of eukaryotic cells dictates the need to compartmentalize various chemical processes within different areas of the cell, using complex membrane-bound organelles. In contrast, prokaryotic cells generally lack membrane-bound organelles; however, they often contain inclusions that compartmentalize their cytoplasm. **[Figure 3.12](#page-112-0)** illustrates structures typically associated with prokaryotic cells. These structures are described in more detail in the next section. \n \n**Figure 3.12** A typical prokaryotic cell contains a cell membrane, chromosomal DNA that is concentrated in a nucleoid, ribosomes, and a cell wall. Some prokaryotic cells may also possess flagella, pili, fimbriae, and capsules.",
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"Header 2": "**3.3 Unique Characteristics of Prokaryotic Cells**",
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"page_content": "Individual cells of a particular prokaryotic organism are typically similar in shape, or **cell morphology**. Although thousands of prokaryotic organisms have been identified, only a handful of cell morphologies are commonly seen microscopically. **[Figure 3.13](#page-113-0)** names and illustrates cell morphologies commonly found in prokaryotic cells. In addition to cellular shape, prokaryotic cells of the same species may group together in certain distinctive arrangements depending on the plane of cell division. Some common arrangements are shown in **[Figure 3.14](#page-114-0)**. \n| | Common Prokaryotic Cell Shapes | | |\n|-------------------------------------|--------------------------------|--------------|--------|\n| Name | Description | Illustration | Image |\n| Coccus
(pl. cocci) | Round | | 200 μm |\n| Bacillus
(pl. bacilli) | Rod | | |\n| Vibrio
(pl. vibrios) | Curved rod | | |\n| Coccobacillus
(pl. coccobacilli) | Short rod | | 1.1. |\n| Spirillum
(pl. spirilla) | Spiral | | A F |\n| Spirochete
(pl. spirochetes) | Long, loose,
helical spiral | m | ~~~ | \n**Figure 3.13** (credit \"Coccus\" micrograph: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit \"Coccobacillus\" micrograph: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit \"Spirochete\" micrograph: modification of work by Centers for Disease Control and Prevention) \n| Common Prokaryotic Cell Arrangements | | |\n|---------------------------------------|---------------------------------------------|--------------|\n| Name | Description | Illustration |\n| Coccus
(pl. cocci) | Single coccus | 0 |\n| Diplococcus
(pl. diplococci) | Pair of two cocci | |\n| Tetrad
(pl. tetrads) | Grouping of four cells arranged in a square | 88 |\n| Streptococcus
(pl. streptococci) | Chain of cocci | 800 |\n| Staphylococcus
(pl. staphylococci) | Cluster of cocci | 033 |\n| Bacillus
(pl. bacilli) | Single rod | |\n| Streptobacillus (pl. streptobacilli) | Chain of rods | | \n**Figure 3.14** \nIn most prokaryotic cells, morphology is maintained by the **cell wall** in combination with cytoskeletal elements. The cell wall is a structure found in most prokaryotes and some eukaryotes; it envelopes the cell membrane, protecting the cell from changes in **osmotic pressure** (**[Figure 3.15](#page-115-0)**). Osmotic pressure occurs because of differences in the concentration of solutes on opposing sides of a semipermeable membrane. Water is able to pass through a semipermeable membrane, but solutes (dissolved molecules like salts, sugars, and other compounds) cannot. When the concentration of solutes is greater on one side of the membrane, water diffuses across the membrane from the side with the lower concentration (more water) to the side with the higher concentration (less water) until the concentrations on both sides become equal. This diffusion of water is called **osmosis**, and it can cause extreme osmotic pressure on a cell when its external environment changes. \nThe external environment of a cell can be described as an isotonic, hypertonic, or hypotonic medium. In an **isotonic medium**, the solute concentrations inside and outside the cell are approximately equal, so there is no net movement of water across the cell membrane. In a **hypertonic medium**, the solute concentration outside the cell exceeds that inside the cell, so water diffuses out of the cell and into the external medium. In a **hypotonic medium**, the solute concentration inside the cell exceeds that outside of the cell, so water will move by osmosis into the cell. This causes the cell to swell and potentially lyse, or burst. \nThe degree to which a particular cell is able to withstand changes in osmotic pressure is called tonicity. Cells that have a cell wall are better able to withstand subtle changes in osmotic pressure and maintain their shape. In hypertonic environments, cells that lack a cell wall can become dehydrated, causing **crenation**, or shriveling of the cell; the plasma membrane contracts and appears scalloped or notched (**[Figure 3.15](#page-115-0)**). By contrast, cells that possess a cell wall undergo **plasmolysis** rather than crenation. In plasmolysis, the plasma membrane contracts and detaches from the cell wall, and there is a decrease in interior volume, but the cell wall remains intact, thus allowing the cell to maintain some shape and integrity for a period of time (**[Figure 3.16](#page-115-1)**). Likewise, cells that lack a cell wall are more prone to lysis in hypotonic environments. The presence of a cell wall allows the cell to maintain its shape and integrity \nfor a longer time before lysing (**[Figure 3.16](#page-115-1)**). \n \n**Figure 3.15** In cells that lack a cell wall, changes in osmotic pressure can lead to crenation in hypertonic environments or cell lysis in hypotonic environments. \n \n**Figure 3.16** In prokaryotic cells, the cell wall provides some protection against changes in osmotic pressure, allowing it to maintain its shape longer. The cell membrane is typically attached to the cell wall in an isotonic medium (left). In a hypertonic medium, the cell membrane detaches from the cell wall and contracts (plasmolysis) as water leaves the cell. In a hypotonic medium (right), the cell wall prevents the cell membrane from expanding to the point of bursting, although lysis will eventually occur if too much water is absorbed. \n \n- Explain the difference between cell morphology and arrangement.\n- What advantages do cell walls provide prokaryotic cells?",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "All cellular life has a DNA genome organized into one or more chromosomes. Prokaryotic chromosomes are typically circular, haploid (unpaired), and not bound by a complex nuclear membrane. Prokaryotic DNA and DNA-associated proteins are concentrated within the **nucleoid** region of the cell (**[Figure 3.17](#page-116-0)**). In general, prokaryotic DNA interacts with **nucleoid-associated proteins (NAPs)** that assist in the organization and packaging of the chromosome. In bacteria, NAPs function similar to histones, which are the DNA-organizing proteins found in eukaryotic cells. In archaea, the nucleoid is organized by either NAPs or histone-like DNA organizing proteins. \n \n**Figure 3.17** The nucleoid region (the area enclosed by the green dashed line) is a condensed area of DNA found within prokaryotic cells. Because of the density of the area, it does not readily stain and appears lighter in color when viewed with a transmission electron microscope.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"Header 3": "**The Nucleoid**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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"page_content": "Prokaryotic cells may also contain extrachromosomal DNA, or DNA that is not part of the chromosome. This extrachromosomal DNA is found in **plasmids**, which are small, circular, double-stranded DNA molecules. Cells that have plasmids often have hundreds of them within a single cell. Plasmids are more commonly found in bacteria; however, plasmids have been found in archaea and eukaryotic organisms. Plasmids often carry genes that confer advantageous traits such as antibiotic resistance; thus, they are important to the survival of the organism. We will discuss plasmids in more detail in **[Mechanisms of Microbial Genetics](#page-452-1)**. \n#### **Ribosomes** \nAll cellular life synthesizes proteins, and organisms in all three domains of life possess ribosomes, structures responsible protein synthesis. However, ribosomes in each of the three domains are structurally different. Ribosomes, themselves, are constructed from proteins, along with ribosomal RNA (rRNA). Prokaryotic ribosomes are found in the cytoplasm. They are called **70S ribosomes** because they have a size of 70S (**[Figure 3.18](#page-117-0)**), whereas eukaryotic cytoplasmic ribosomes have a size of 80S. (The S stands for Svedberg unit, a measure of sedimentation in an ultracentrifuge, which is based on size, shape, and surface qualities of the structure being analyzed). Although they are the same size, bacterial and archaeal ribosomes have different proteins and rRNA molecules, and the archaeal versions are more similar to their eukaryotic counterparts than to those found in bacteria. \n \n**Figure 3.18** Prokaryotic ribosomes (70S) are composed of two subunits: the 30S (small subunit) and the 50S (large subunit), each of which are composed of protein and rRNA components.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"Header 3": "**Plasmids**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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"page_content": "As single-celled organisms living in unstable environments, some prokaryotic cells have the ability to store excess nutrients within cytoplasmic structures called **inclusions**. Storing nutrients in a polymerized form is advantageous because it reduces the buildup of osmotic pressure that occurs as a cell accumulates solutes. Various types of inclusions store glycogen and starches, which contain carbon that cells can access for energy. **Volutin** granules, also called **metachromatic granules** because of their staining characteristics, are inclusions that store polymerized inorganic phosphate that can be used in metabolism and assist in the formation of biofilms. Microbes known to contain volutin granules include the archaea *Methanosarcina*, the bacterium *Corynebacterium diphtheriae*, and the unicellular eukaryotic alga *Chlamydomonas*. Sulfur granules, another type of inclusion, are found in sulfur bacteria of the genus *Thiobacillus*; these granules store elemental sulfur, which the bacteria use for metabolism. \nOccasionally, certain types of inclusions are surrounded by a phospholipid monolayer embedded with protein. **Polyhydroxybutyrate (PHB)**, which can be produced by species of *Bacillus* and *Pseudomonas*, is an example of an inclusion that displays this type of monolayer structure. Industrially, PHB has also been used as a source of biodegradable polymers for bioplastics. Several different types of inclusions are shown in **[Figure 3.19](#page-118-0)**. \n**Figure 3.19** Prokaryotic cells may have various types of inclusions. (a) A transmission electron micrograph of polyhydroxybutryrate lipid droplets. (b) A light micrograph of volutin granules. (c) A phase-contrast micrograph of sulfur granules. (d) A transmission electron micrograph of magnetosomes. (e) A transmission electron micrograph of gas vacuoles. (credit b, c, d: modification of work by American Society for Microbiology) \nSome prokaryotic cells have other types of inclusions that serve purposes other than nutrient storage. For example, some prokaryotic cells produce gas vacuoles, accumulations of small, protein-lined vesicles of gas. These gas vacuoles allow the prokaryotic cells that synthesize them to alter their buoyancy so that they can adjust their location in the water column. Magnetotactic bacteria, such as *Magnetospirillum magnetotacticum*, contain **magnetosomes**, which are inclusions of magnetic iron oxide or iron sulfide surrounded by a lipid layer. These allow cells to align along a magnetic field, aiding their movement (**[Figure 3.19](#page-118-0)**). Cyanobacteria such as *Anabaena cylindrica* and bacteria such as *Halothiobacillus neapolitanus* produce **carboxysome** inclusions. Carboxysomes are composed of outer shells of thousands of protein subunits. Their interior is filled with ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. Both of these compounds are used for carbon metabolism. Some prokaryotic cells also possess carboxysomes that sequester functionally related enzymes in one location. These structures are considered proto-organelles because they compartmentalize important compounds or chemical reactions, much like many eukaryotic organelles.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"Header 3": "**Inclusions**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "Bacterial cells are generally observed as **vegetative cells**, but some genera of bacteria have the ability to form **endospores**, structures that essentially protect the bacterial genome in a dormant state when environmental conditions are unfavorable. Endospores (not to be confused with the reproductive spores formed by fungi) allow some bacterial cells to survive long periods without food or water, as well as exposure to chemicals, extreme temperatures, and even radiation. **[Table 3.1](#page-119-0)** compares the characteristics of vegetative cells and endospores. \n#### **Characteristics of Vegetative Cells versus Endospores** \n| Vegetative Cells | Endospores |\n|----------------------------------------------------|-------------------------------------------------------------------------------------------------|\n| Sensitive to extreme temperatures
and radiation | Resistant to extreme temperatures and radiation |\n| Gram-positive | Do not absorb Gram stain, only special endospore stains (see Staining
Microscopic Specimens) |\n| Normal water content and
enzymatic activity | Dehydrated; no metabolic activity |\n| Capable of active growth and
metabolism | Dormant; no growth or metabolic activity | \n#### **Table 3.1** \nThe process by which vegetative cells transform into endospores is called **sporulation**, and it generally begins when nutrients become depleted or environmental conditions become otherwise unfavorable (**[Figure 3.20](#page-120-0)**). The process begins with the formation of a septum in the vegetative bacterial cell. The septum divides the cell asymmetrically, separating a DNA forespore from the mother cell. The forespore, which will form the core of the endospore, is essentially a copy of the cell's chromosomes, and is separated from the mother cell by a second membrane. A cortex gradually forms around the forespore by laying down layers of calcium and dipicolinic acid between membranes. A protein spore coat then forms around the cortex while the DNA of the mother cell disintegrates. Further maturation of the endospore occurs with the formation of an outermost exosporium. The endospore is released upon disintegration of the mother cell, completing sporulation. \n \n**Figure 3.20** (a) Sporulation begins following asymmetric cell division. The forespore becomes surrounded by a double layer of membrane, a cortex, and a protein spore coat, before being released as a mature endospore upon disintegration of the mother cell. (b) An electron micrograph of a *Carboxydothermus hydrogenoformans* endospore. (c) These *Bacillus spp.* cells are undergoing sporulation. The endospores have been visualized using Malachite Green spore stain. (credit b: modification of work by Jonathan Eisen) \nEndospores of certain species have been shown to persist in a dormant state for extended periods of time, up to thousands of years.[17] However, when living conditions improve, endospores undergo **germination**, reentering a vegetative state. After germination, the cell becomes metabolically active again and is able to carry out all of its normal functions, including growth and cell division. \nNot all bacteria have the ability to form endospores; however, there are a number of clinically significant endosporeforming gram-positive bacteria of the genera *Bacillus* and *Clostridium*. These include *B. anthracis*, the causative agent of anthrax, which produces endospores capable of survive for many decades[18]; *C. tetani* (causes tetanus); *C. difficile* (causes pseudomembranous colitis); *C. perfringens* (causes gas gangrene); and *C. botulinum* (causes botulism). Pathogens such as these are particularly difficult to combat because their endospores are so hard to kill. Special sterilization methods for endospore-forming bacteria are discussed in **[Control of Microbial Growth](#page-560-1)**. \n \n- What is an inclusion?\n- What is the function of an endospore? \n17. F. Rothfuss, M Bender, R Conrad. \"Survival and Activity of Bacteria in a Deep, Aged Lake Sediment (Lake Constance).\" *Microbial Ecology* 33 no. 1 (1997):69–77. \n18. R. Sinclair et al. \"Persistence of Category A Select Agents in the Environment.\" *Applied and Environmental Microbiology* 74 no. 3 (2008):555–563.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Endospores**",
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"page_content": "Structures that enclose the cytoplasm and internal structures of the cell are known collectively as the **cell envelope**. In prokaryotic cells, the structures of the cell envelope vary depending on the type of cell and organism. Most (but not all) prokaryotic cells have a cell wall, but the makeup of this cell wall varies. All cells (prokaryotic and eukaryotic) have a **plasma membrane** (also called **cytoplasmic membrane** or **cell membrane**) that exhibits selective permeability, allowing some molecules to enter or leave the cell while restricting the passage of others. \nThe structure of the plasma membrane is often described in terms of the **fluid mosaic model**, which refers to the ability of membrane components to move fluidly within the plane of the membrane, as well as the mosaic-like composition of the components, which include a diverse array of lipid and protein components (**[Figure 3.21](#page-121-0)**). The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. These phospholipids and proteins have the ability to move laterally within the plane of the membranes as well as between the two phospholipid layers. \n \n**Figure 3.21** The bacterial plasma membrane is a phospholipid bilayer with a variety of embedded proteins that perform various functions for the cell. Note the presence of glycoproteins and glycolipids, whose carbohydrate components extend out from the surface of the cell. The abundance and arrangement of these proteins and lipids can vary greatly between species. \nArchaeal membranes are fundamentally different from bacterial and eukaryotic membranes in a few significant ways. First, archaeal membrane phospholipids are formed with ether linkages, in contrast to the ester linkages found in bacterial or eukaryotic cell membranes. Second, archaeal phospholipids have branched chains, whereas those of bacterial and eukaryotic cells are straight chained. Finally, although some archaeal membranes can be formed of bilayers like those found in bacteria and eukaryotes, other archaeal plasma membranes are lipid monolayers. \nProteins on the cell's surface are important for a variety of functions, including cell-to-cell communication, and sensing environmental conditions and pathogenic virulence factors. Membrane proteins and phospholipids may have carbohydrates (sugars) associated with them and are called glycoproteins or glycolipids, respectively. These glycoprotein and glycolipid complexes extend out from the surface of the cell, allowing the cell to interact with the external environment (**[Figure 3.21](#page-121-0)**). Glycoproteins and glycolipids in the plasma membrane can vary considerably in chemical composition among archaea, bacteria, and eukaryotes, allowing scientists to use them to characterize unique species. \nPlasma membranes from different cells types also contain unique phospholipids, which contain fatty acids. As described in **[Using Biochemistry to Identify Microorganisms](#page-314-0)**, phospholipid-derived fatty acid analysis (PLFA) profiles can be used to identify unique types of cells based on differences in fatty acids. Archaea, bacteria, and eukaryotes each have a unique PFLA profile. \n#### **Membrane Transport Mechanisms** \nOne of the most important functions of the plasma membrane is to control the transport of molecules into and out of the cell. Internal conditions must be maintained within a certain range despite any changes in the external environment. The transport of substances across the plasma membrane allows cells to do so. \nCells use various modes of transport across the plasma membrane. For example, molecules moving from a higher concentration to a lower concentration with the concentration gradient are transported by simple diffusion, also known as passive transport (**[Figure 3.22](#page-122-0)**). Some small molecules, like carbon dioxide, may cross the membrane bilayer directly by simple diffusion. However, charged molecules, as well as large molecules, need the help of carriers or channels in the membrane. These structures ferry molecules across the membrane, a process known as facilitated diffusion (**[Figure 3.23](#page-123-0)**). \nActive transport occurs when cells move molecules across their membrane *against* concentration gradients (**[Figure](#page-123-1) [3.24](#page-123-1)**). A major difference between passive and active transport is that active transport requires adenosine triphosphate (ATP) or other forms of energy to move molecules \"uphill.\" Therefore, active transport structures are often called \"pumps.\" \n \n**Figure 3.22** Simple diffusion down a concentration gradient directly across the phospholipid bilayer. (credit: modification of work by Mariana Ruiz Villareal) \n \n**Figure 3.23** Facilitated diffusion down a concentration gradient through a membrane protein. (credit: modification of work by Mariana Ruiz Villareal) \n \n**Figure 3.24** Active transport against a concentration gradient via a membrane pump that requires energy. (credit: modification of work by Mariana Ruiz Villareal) \nGroup translocation also transports substances into bacterial cells. In this case, as a molecule moves into a cell against its concentration gradient, it is chemically modified so that it does not require transport against an unfavorable concentration gradient. A common example of this is the bacterial phosphotransferase system, a series of carriers that phosphorylates (i.e., adds phosphate ions to) glucose or other sugars upon entry into cells. Since the phosphorylation of sugars is required during the early stages of sugar metabolism, the phosphotransferase system is considered to be an energy neutral system. \n#### **Photosynthetic Membrane Structures** \nSome prokaryotic cells, namely cyanobacteria and photosynthetic bacteria, have membrane structures that enable them to perform photosynthesis. These structures consist of an infolding of the plasma membrane that encloses photosynthetic pigments such as green **chlorophylls** and bacteriochlorophylls. In cyanobacteria, these membrane structures are called thylakoids; in photosynthetic bacteria, they are called chromatophores, lamellae, or chlorosomes. \n#### **Cell Wall** \nThe primary function of the cell wall is to protect the cell from harsh conditions in the outside environment. When \npresent, there are notable similarities and differences among the cell walls of archaea, bacteria, and eukaryotes. \nThe major component of bacterial cell walls is called **peptidoglycan** (or murein); it is only found in bacteria. Structurally, peptidoglycan resembles a layer of meshwork or fabric (**[Figure 3.25](#page-124-0)**). Each layer is composed of long chains of alternating molecules of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). The structure of the long chains has significant two-dimensional tensile strength due to the formation of peptide bridges that connect NAG and NAM within each peptidoglycan layer. In gram-negative bacteria, tetrapeptide chains extending from each NAM unit are directly cross-linked, whereas in gram-positive bacteria, these tetrapeptide chains are linked by pentaglycine cross-bridges. Peptidoglycan subunits are made inside of the bacterial cell and then exported and assembled in layers, giving the cell its shape. \nSince peptidoglycan is unique to bacteria, many antibiotic drugs are designed to interfere with peptidoglycan synthesis, weakening the cell wall and making bacterial cells more susceptible to the effects of osmotic pressure (see **[Mechanisms of Antibacterial Drugs](#page-622-0)**). In addition, certain cells of the human immune system are able \"recognize\" bacterial pathogens by detecting peptidoglycan on the surface of a bacterial cell; these cells then engulf and destroy the bacterial cell, using enzymes such as lysozyme, which breaks down and digests the peptidoglycan in their cell walls (see **[Pathogen Recognition and Phagocytosis](#page-765-0)**). \n \n**Figure 3.25** Peptidoglycan is composed of polymers of alternating NAM and NAG subunits, which are cross-linked by peptide bridges linking NAM subunits from various glycan chains. This provides the cell wall with tensile strength in two dimensions. \nThe Gram staining protocol (see **[Staining Microscopic Specimens](#page-80-0)**) is used to differentiate two common types of cell wall structures (**[Figure 3.26](#page-125-0)**). Gram-positive cells have a cell wall consisting of many layers of peptidoglycan totaling 30–100 nm in thickness. These peptidoglycan layers are commonly embedded with teichoic acids (TAs), carbohydrate chains that extend through and beyond the peptidoglycan layer.[19] TA is thought to stabilize peptidoglycan by increasing its rigidity. TA also plays a role in the ability of pathogenic gram-positive bacteria such as *Streptococcus* to bind to certain proteins on the surface of host cells, enhancing their ability to cause infection. In addition to peptidoglycan and TAs, bacteria of the family Mycobacteriaceae have an external layer of waxy **mycolic acids** in their cell wall; as described in **[Staining Microscopic Specimens](#page-80-0)**, these bacteria are referred to as acidfast, since acid-fast stains must be used to penetrate the mycolic acid layer for purposes of microscopy (**[Figure 3.27](#page-125-1)**). \n \n**Figure 3.26** Bacteria contain two common cell wall structural types. Gram-positive cell walls are structurally simple, containing a thick layer of peptidoglycan with embedded teichoic acid external to the plasma membrane.[20] Gramnegative cell walls are structurally more complex, containing three layers: the inner membrane, a thin layer of peptidoglycan, and an outer membrane containing lipopolysaccharide. (credit: modification of work by \"Franciscosp2\"/Wikimedia Commons) \n \n**Figure 3.27** (a) Some gram-positive bacteria, including members of the Mycobacteriaceae, produce waxy mycolic acids found exterior to their structurally-distinct peptidoglycan. (b) The acid-fast staining protocol detects the presence of cell walls that are rich in mycolic acid. Acid-fast cells are stained red by carbolfuschin. (credit a: modification of work by \"Franciscosp2\"/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention) \nGram-negative cells have a much thinner layer of peptidoglycan (no more than about 4 nm thick[21]) than grampositive cells, and the overall structure of their cell envelope is more complex. In gram-negative cells, a gel-like matrix occupies the **periplasmic space** between the cell wall and the plasma membrane, and there is a second lipid bilayer called the **outer membrane**, which is external to the peptidoglycan layer (**[Figure 3.26](#page-125-0)**). This outer membrane is attached to the peptidoglycan by murein lipoprotein. The outer leaflet of the outer membrane contains the molecule **lipopolysaccharide (LPS)**, which functions as an endotoxin in infections involving gram-negative bacteria, contributing to symptoms such as fever, hemorrhaging, and septic shock. Each LPS molecule is composed \n20. B. Zuber et al. \"Granular Layer in the Periplasmic Space of Gram-Positive Bacteria and Fine Structures of *Enterococcus gallinarum* and *Streptococcus gordonii* Septa Revealed by Cryo-Electron Microscopy of Vitreous Sections.\" *Journal of Bacteriology* 188 no. 18 (2006):6652–6660 \n21. L. Gana, S. Chena, G.J. Jensena. \"Molecular Organization of Gram-Negative Peptidoglycan.\" *Proceedings of the National Academy of Sciences of the United States of America* 105 no. 48 (2008):18953–18957. \nof Lipid A, a core polysaccharide, and an O side chain that is composed of sugar-like molecules that comprise the external face of the LPS (**[Figure 3.28](#page-126-0)**). The composition of the O side chain varies between different species and strains of bacteria. Parts of the O side chain called antigens can be detected using serological or immunological tests to identify specific pathogenic strains like *Escherichia coli* O157:H7, a deadly strain of bacteria that causes bloody diarrhea and kidney failure. \n \n**Figure 3.28** The outer membrane of a gram-negative bacterial cell contains lipopolysaccharide (LPS), a toxin composed of Lipid A embedded in the outer membrane, a core polysaccharide, and the O side chain. \nArchaeal cell wall structure differs from that of bacteria in several significant ways. First, archaeal cell walls do not contain peptidoglycan; instead, they contain a similar polymer called pseudopeptidoglycan (pseudomurein) in which NAM is replaced with a different subunit. Other archaea may have a layer of glycoproteins or polysaccharides that serves as the cell wall instead of pseudopeptidoglycan. Last, as is the case with some bacterial species, there are a few archaea that appear to lack cell walls entirely.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Endospores**",
"Header 3": "**Plasma Membrane**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "Although most prokaryotic cells have cell walls, some may have additional cell envelope structures exterior to the cell wall, such as glycocalyces and S-layers. A **glycocalyx** is a sugar coat, of which there are two important types: capsules and slime layers. A **capsule** is an organized layer located outside of the cell wall and usually composed of polysaccharides or proteins (**[Figure 3.29](#page-127-1)**). A **slime layer** is a less tightly organized layer that is only loosely attached to the cell wall and can be more easily washed off. Slime layers may be composed of polysaccharides, glycoproteins, or glycolipids. \nGlycocalyces allows cells to adhere to surfaces, aiding in the formation of biofilms (colonies of microbes that form in layers on surfaces). In nature, most microbes live in mixed communities within biofilms, partly because the biofilm affords them some level of protection. Biofilms generally hold water like a sponge, preventing desiccation. They also protect cells from predation and hinder the action of antibiotics and disinfectants. All of these properties are advantageous to the microbes living in a biofilm, but they present challenges in a clinical setting, where the goal is \noften to eliminate microbes. \n \n**Figure 3.29** (a) Capsules are a type of glycocalyx composed of an organized layer of polysaccharides. (b) A capsule stain of *Pseudomonas aeruginosa*, a bacterial pathogen capable of causing many different types of infections in humans. (credit b: modification of work by American Society for Microbiology) \nThe ability to produce a capsule can contribute to a microbe's pathogenicity (ability to cause disease) because the capsule can make it more difficult for phagocytic cells (such as white blood cells) to engulf and kill the microorganism. *Streptococcus pneumoniae*, for example, produces a capsule that is well known to aid in this bacterium's pathogenicity. As explained in **[Staining Microscopic specimens](#page-80-0)**, capsules are difficult to stain for microscopy; negative staining techniques are typically used. \nAn **S-layer** is another type of cell envelope structure; it is composed of a mixture of structural proteins and glycoproteins. In bacteria, S-layers are found outside the cell wall, but in some archaea, the S-layer serves *as* the cell wall. The exact function of S-layers is not entirely understood, and they are difficult to study; but available evidence suggests that they may play a variety of functions in different prokaryotic cells, such as helping the cell withstand osmotic pressure and, for certain pathogens, interacting with the host immune system. \n#### **Clinical Focus** \n#### **Part 3** \nAfter diagnosing Barbara with pneumonia, the PA writes her a prescription for amoxicillin, a commonlyprescribed type of penicillin derivative. More than a week later, despite taking the full course as directed, Barbara still feels weak and is not fully recovered, although she is still able to get through her daily activities. She returns to the health center for a follow-up visit. \nMany types of bacteria, fungi, and viruses can cause pneumonia. Amoxicillin targets the peptidoglycan of bacterial cell walls. Since the amoxicillin has not resolved Barbara's symptoms, the PA concludes that the causative agent probably lacks peptidoglycan, meaning that the pathogen could be a virus, a fungus, or a bacterium that lacks peptidoglycan. Another possibility is that the pathogen is a bacterium containing peptidoglycan but has developed resistance to amoxicillin. \n- How can the PA definitively identify the cause of Barbara's pneumonia?\n- What form of treatment should the PA prescribe, given that the amoxicillin was ineffective? \n*Jump to the [next](#page-150-0) Clinical Focus box. Go back to the [previous](#page-109-0) Clinical Focus box.*",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Glycocalyces and S-Layers**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "Many bacterial cells have protein appendages embedded within their cell envelopes that extend outward, allowing interaction with the environment. These appendages can attach to other surfaces, transfer DNA, or provide movement. Filamentous appendages include fimbriae, pili, and flagella. \n#### **Fimbriae and Pili** \nFimbriae and pili are structurally similar and, because differentiation between the two is problematic, these terms are often used interchangeably.[22] [23] The term **fimbriae** commonly refers to short bristle-like proteins projecting from the cell surface by the hundreds. Fimbriae enable a cell to attach to surfaces and to other cells. For pathogenic bacteria, adherence to host cells is important for colonization, infectivity, and virulence. Adherence to surfaces is also important in biofilm formation. \nThe term **pili** (singular: pilus) commonly refers to longer, less numerous protein appendages that aid in attachment to surfaces (**[Figure 3.30](#page-128-0)**). A specific type of pilus, called the **F pilus** or **sex pilus**, is important in the transfer of DNA between bacterial cells, which occurs between members of the same generation when two cells physically transfer or exchange parts of their respective genomes (see **[How Asexual Prokaryotes Achieve Genetic Diversity](#page-487-0)**). \n \n**Figure 3.30** Bacteria may produce two different types of protein appendages that aid in surface attachment. Fimbriae typically are more numerous and shorter, whereas pili (shown here) are longer and less numerous per cell. (credit: modification of work by American Society for Microbiology) \n#### **Micro Connections** \n#### **Group A Strep** \nBefore the structure and function of the various components of the bacterial cell envelope were well understood, scientists were already using cell envelope characteristics to classify bacteria. In 1933, Rebecca Lancefield proposed a method for serotyping various β-hemolytic strains of *Streptococcus* species using an agglutination assay, a technique using the clumping of bacteria to detect specific cell-surface antigens. In doing so, Lancefield discovered that one group of *S. pyogenes*, found in Group A, was associated with a variety of human diseases. She determined that various strains of Group A strep could be distinguished from each other based on variations in specific cell surface proteins that she named M proteins. \nToday, more than 80 different strains of Group A strep have been identified based on M proteins. Various strains of Group A strep are associated with a wide variety of human infections, including streptococcal \n22. J.A. Garnetta et al. \"Structural Insights Into the Biogenesis and Biofilm Formation by the *Escherichia coli* Common Pilus.\" *Proceedings of the National Academy of Sciences of the United States of America* 109 no. 10 (2012):3950–3955. \n23. T. Proft, E.N. Baker. \"Pili in Gram-Negative and Gram-Positive Bacteria—Structure, Assembly and Their Role in Disease.\" *Cellular and Molecular Life Sciences* 66 (2009):613. \npharyngitis (strep throat), impetigo, toxic shock syndrome, scarlet fever, rheumatic fever, and necrotizing fasciitis. The M protein is an important virulence factor for Group A strep, helping these strains evade the immune system. Changes in M proteins appear to alter the infectivity of a particular strain of Group A strep. \n#### **Flagella** \n**Flagella** are structures used by cells to move in aqueous environments. Bacterial flagella act like propellers. They are stiff spiral filaments composed of flagellin protein subunits that extend outward from the cell and spin in solution. The **basal body** is the motor for the flagellum and is embedded in the plasma membrane (**[Figure 3.31](#page-129-0)**). A hook region connects the basal body to the filament. Gram-positive and gram-negative bacteria have different basal body configurations due to differences in cell wall structure. \nDifferent types of motile bacteria exhibit different arrangements of flagella (**[Figure 3.32](#page-130-0)**). A bacterium with a singular flagellum, typically located at one end of the cell (polar), is said to have a **monotrichous** flagellum. An example of a monotrichously flagellated bacterial pathogen is *Vibrio cholerae*, the gram-negative bacterium that causes cholera. Cells with **amphitrichous** flagella have a flagellum or tufts of flagella at each end. An example is *Spirillum minor*, the cause of spirillary (Asian) rat-bite fever or sodoku. Cells with **lophotrichous** flagella have a tuft at one end of the cell. The gram-negative bacillus *Pseudomonas aeruginosa*, an opportunistic pathogen known for causing many infections, including \"swimmer's ear\" and burn wound infections, has lophotrichous flagella. Flagella that cover the entire surface of a bacterial cell are called **peritrichous** flagella. The gram-negative bacterium *E. coli* shows a peritrichous arrangement of flagella. \n \n**Figure 3.31** The basic structure of a bacterial flagellum consists of a basal body, hook, and filament. The basal body composition and arrangement differ between gram-positive and gram-negative bacteria. (credit: modification of work by \"LadyofHats\"/Mariana Ruiz Villareal) \n \n**Figure 3.32** Flagellated bacteria may exhibit multiple arrangements of their flagella. Common arrangements include monotrichous, amphitrichous, lophotrichous, or peritrichous. \nDirectional movement depends on the configuration of the flagella. Bacteria can move in response to a variety of environmental signals, including light (**phototaxis**), magnetic fields (**magnetotaxis**) using magnetosomes, and, most commonly, chemical gradients (**chemotaxis**). Purposeful movement toward a chemical attractant, like a food source, or away from a repellent, like a poisonous chemical, is achieved by increasing the length of **runs** and decreasing the length of **tumbles**. When running, flagella rotate in a counterclockwise direction, allowing the bacterial cell to move forward. In a peritrichous bacterium, the flagella are all bundled together in a very streamlined way (**[Figure 3.33](#page-130-1)**), allowing for efficient movement. When tumbling, flagella are splayed out while rotating in a clockwise direction, creating a looping motion and preventing meaningful forward movement but reorienting the cell toward the direction of the attractant. When an attractant exists, runs and tumbles still occur; however, the length of runs is longer, while the length of the tumbles is reduced, allowing overall movement toward the higher concentration of the attractant. When no chemical gradient exists, the lengths of runs and tumbles are more equal, and overall movement is more random (**[Figure 3.34](#page-131-1)**). \n \n**Figure 3.33** Bacteria achieve directional movement by changing the rotation of their flagella. In a cell with peritrichous flagella, the flagella bundle when they rotate in a counterclockwise direction, resulting in a run. However, when the flagella rotate in a clockwise direction, the flagella are no longer bundled, resulting in tumbles. \n \n**Figure 3.34** Without a chemical gradient, flagellar rotation cycles between counterclockwise (run) and clockwise (tumble) with no overall directional movement. However, when a chemical gradient of an attractant exists, the length of runs is extended, while the length of tumbles is decreased. This leads to chemotaxis: an overall directional movement toward the higher concentration of the attractant. \n \n- What is the peptidoglycan layer and how does it differ between gram-positive and gram-negative bacteria?\n- Compare and contrast monotrichous, amphitrichous, lophotrichous, and peritrichous flagella.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Glycocalyces and S-Layers**",
"Header 3": "**Filamentous Appendages**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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"page_content": "#### **Learning Objectives** \n- Explain the distinguishing characteristics of eukaryotic cells\n- Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function\n- Identify and describe structures and organelles unique to eukaryotic cells\n- Compare and contrast similar structures found in prokaryotic and eukaryotic cells \nEukaryotic organisms include protozoans, algae, fungi, plants, and animals. Some eukaryotic cells are independent, single-celled microorganisms, whereas others are part of multicellular organisms. The cells of eukaryotic organisms have several distinguishing characteristics. Above all, eukaryotic cells are defined by the presence of a nucleus surrounded by a complex nuclear membrane. Also, eukaryotic cells are characterized by the presence of membranebound organelles in the cytoplasm. Organelles such as mitochondria, the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes are held in place by the **cytoskeleton**, an internal network that supports \ntransport of intracellular components and helps maintain cell shape (**[Figure 3.35](#page-132-0)**). The genome of eukaryotic cells is packaged in multiple, rod-shaped chromosomes as opposed to the single, circular-shaped chromosome that characterizes most prokaryotic cells. **[Table 3.2](#page-132-1)** compares the characteristics of eukaryotic cell structures with those of bacteria and archaea. \n \n**Figure 3.35** An illustration of a generalized, single-celled eukaryotic organism. Note that cells of eukaryotic organisms vary greatly in terms of structure and function, and a particular cell may not have all of the structures shown here. \n#### **Summary of Cell Structures** \n| Cell Structure | Prokaryotes | | Eukaryotes |\n|---------------------------------|-------------|-----------|------------|\n| | Bacteria | Archaea | |\n| Size | ~0.5–1 μM | ~0.5–1 μM | ~5–20 μM |\n| Surface area-to
volume ratio | High | High | Low |\n| Nucleus | No | No | Yes | \n**Table 3.2** \n#### **Summary of Cell Structures** \n| Cell Structure | Prokaryotes | | Eukaryotes |\n|---------------------------------|--------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| | Bacteria | Archaea | |\n| Genome
characteristics | •
Single chromosome
•
Circular
•
Haploid
•
Lacks histones | •
Single chromosome
•
Circular
•
Haploid
•
Contains histones | •
Multiple chromosomes
•
Linear
•
Haploid or diploid
•
Contains histones |\n| Cell division | Binary fission | Binary fission | Mitosis, meiosis |\n| Membrane lipid
composition | •
Ester-linked
•
Straight-chain fatty
acids
•
Bilayer | •
Ether-linked
•
Branched isoprenoids
•
Bilayer or monolayer | •
Ester-linked
•
Straight-chain fatty acids
•
Sterols
•
Bilayer |\n| Cell wall
composition | •
Peptidoglycan, or
•
None | •
Pseudopeptidoglycan, or
•
Glycopeptide, or
•
Polysaccharide, or
•
Protein (S-layer), or
•
None | •
Cellulose (plants, some
algae)
•
Chitin (molluscs, insects,
crustaceans, and fungi)
•
Silica (some algae)
•
Most others lack cell walls |\n| Motility
structures | Rigid spiral flagella
composed of flagellin | Rigid spiral flagella composed
of archaeal flagellins | Flexible flagella and cilia
composed of microtubules |\n| Membrane
bound
organelles | No | No | Yes |\n| Endomembrane
system | No | No | Yes (ER, Golgi, lysosomes) |\n| Ribosomes | 70S | 70S | •
80S in cytoplasm and
rough ER
•
70S in mitochondria,
chloroplasts | \n**Table 3.2**",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**3.4 Unique Characteristics of Eukaryotic Cells**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "Eukaryotic cells display a wide variety of different cell morphologies. Possible shapes include spheroid, ovoid, cuboidal, cylindrical, flat, lenticular, fusiform, discoidal, crescent, ring stellate, and polygonal (**[Figure 3.36](#page-134-0)**). Some eukaryotic cells are irregular in shape, and some are capable of changing shape. The shape of a particular type of eukaryotic cell may be influenced by factors such as its primary function, the organization of its cytoskeleton, the viscosity of its cytoplasm, the rigidity of its cell membrane or cell wall (if it has one), and the physical pressure exerted on it by the surrounding environment and/or adjoining cells. \n \n**Figure 3.36** Eukaryotic cells come in a variety of cell shapes. (a) Spheroid *Chromulina* alga. (b) Fusiform shaped *Trypanosoma*. (c) Bell-shaped *Vorticella*. (d) Ovoid *Paramecium*. (e) Ring-shaped *Plasmodium ovale*. (credit a: modification of work by NOAA; credit b, e: modification of work by Centers for Disease Control and Prevention) \n \n• Identify two differences between eukaryotic and prokaryotic cells. \n#### **Nucleus** \nUnlike prokaryotic cells, in which DNA is loosely contained in the nucleoid region, eukaryotic cells possess a **nucleus**, which is surrounded by a complex nuclear membrane that houses the DNA genome (**[Figure 3.37](#page-135-0)**). By containing the cell's DNA, the nucleus ultimately controls all activities of the cell and also serves an essential role in reproduction and heredity. Eukaryotic cells typically have their DNA organized into multiple linear chromosomes. The DNA within the nucleus is highly organized and condensed to fit inside the nucleus, which is accomplished by wrapping the DNA around proteins called histones. \n \n**Figure 3.37** Eukaryotic cells have a well-defined nucleus. The nucleus of this mammalian lung cell is the large, dark, oval-shaped structure in the lower half of the image. \nAlthough most eukaryotic cells have only one nucleus, exceptions exist. For example, protozoans of the genus *Paramecium* typically have two complete nuclei: a small nucleus that is used for reproduction (micronucleus) and a large nucleus that directs cellular metabolism (macronucleus). Additionally, some fungi transiently form cells with two nuclei, called heterokaryotic cells, during sexual reproduction. Cells whose nuclei divide, but whose cytoplasm does not, are called **coenocytes**. \nThe nucleus is bound by a complex **nuclear membrane**, often called the **nuclear envelope**, that consists of two distinct lipid bilayers that are contiguous with each other (**[Figure 3.38](#page-135-1)**). Despite these connections between the inner and outer membranes, each membrane contains unique lipids and proteins on its inner and outer surfaces. The nuclear envelope contains nuclear pores, which are large, rosette-shaped protein complexes that control the movement of materials into and out of the nucleus. The overall shape of the nucleus is determined by the **nuclear lamina**, a meshwork of intermediate filaments found just inside the nuclear envelope membranes. Outside the nucleus, additional intermediate filaments form a looser mesh and serve to anchor the nucleus in position within the cell. \n \n**Figure 3.38** In this fluorescent microscope image, all the intermediate filaments have been stained with a bright green fluorescent stain. The nuclear lamina is the intense bright green ring around the faint red nuclei. \n#### **Nucleolus** \nThe **nucleolus** is a dense region within the nucleus where ribosomal RNA (rRNA) biosynthesis occurs. In addition, the nucleolus is also the site where assembly of ribosomes begins. Preribosomal complexes are assembled from rRNA and proteins in the nucleolus; they are then transported out to the cytoplasm, where ribosome assembly is completed (**[Figure 3.39](#page-136-0)**). \n \n**Figure 3.39** (a) The nucleolus is the dark, dense area within the nucleus. It is the site of rRNA synthesis and preribosomal assembly. (b) Electron micrograph showing the nucleolus.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Cell Morphologies**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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"page_content": "Ribosomes found in eukaryotic organelles such as mitochondria or chloroplasts have 70S ribosomes—the same size as prokaryotic ribosomes. However, nonorganelle-associated ribosomes in eukaryotic cells are **80S ribosomes**, composed of a 40S small subunit and a 60S large subunit. In terms of size and composition, this makes them distinct from the ribosomes of prokaryotic cells. \nThe two types of nonorganelle-associated eukaryotic ribosomes are defined by their location in the cell: **free ribosomes** and **membrane-bound ribosomes**. Free ribosomes are found in the cytoplasm and serve to synthesize water-soluble proteins; membrane-bound ribosomes are found attached to the rough endoplasmic reticulum and make proteins for insertion into the cell membrane or proteins destined for export from the cell. \nThe differences between eukaryotic and prokaryotic ribosomes are clinically relevant because certain antibiotic drugs are designed to target one or the other. For example, cycloheximide targets eukaryotic action, whereas chloramphenicol targets prokaryotic ribosomes.[24] Since human cells are eukaryotic, they generally are not harmed by antibiotics that destroy the prokaryotic ribosomes in bacteria. However, sometimes negative side effects may occur because mitochondria in human cells contain prokaryotic ribosomes.",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Cell Morphologies**",
"Header 3": "**Ribosomes**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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"page_content": "The **endomembrane system**, unique to eukaryotic cells, is a series of membranous tubules, sacs, and flattened disks that synthesize many cell components and move materials around within the cell (**[Figure 3.40](#page-137-0)**). Because of their larger cell size, eukaryotic cells require this system to transport materials that cannot be dispersed by diffusion alone. The endomembrane system comprises several organelles and connections between them, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles. \n \n**Figure 3.40** The endomembrane system is composed of a series of membranous intracellular structures that facilitate movement of materials throughout the cell and to the cell membrane. \n#### **Endoplasmic Reticulum** \nThe **endoplasmic reticulum (ER)** is an interconnected array of tubules and **cisternae** (flattened sacs) with a single lipid bilayer (**[Figure 3.41](#page-137-1)**). The spaces inside of the cisternae are called **lumen** of the ER. There are two types of ER, **rough endoplasmic reticulum (RER)** and **smooth endoplasmic reticulum (SER)**. These two different types of ER are sites for the synthesis of distinctly different types of molecules. RER is studded with ribosomes bound on the cytoplasmic side of the membrane. These ribosomes make proteins destined for the plasma membrane (**[Figure 3.41](#page-137-1)**). Following synthesis, these proteins are inserted into the membrane of the RER. Small sacs of the RER containing these newly synthesized proteins then bud off as **transport vesicles** and move either to the Golgi apparatus for further processing, directly to the plasma membrane, to the membrane of another organelle, or out of the cell. Transport vesicles are single-lipid, bilayer, membranous spheres with hollow interiors that carry molecules. SER does not have ribosomes and, therefore, appears \"smooth.\" It is involved in biosynthesis of lipids, carbohydrate metabolism, and detoxification of toxic compounds within the cell. \n \n**Figure 3.41** The rough endoplasmic reticulum is studded with ribosomes for the synthesis of membrane proteins (which give it its rough appearance). \n#### **Golgi Apparatus** \nThe Golgi apparatus was discovered within the endomembrane system in 1898 by Italian scientist Camillo Golgi (1843–1926), who developed a novel staining technique that showed stacked membrane structures within the cells of *Plasmodium*, the causative agent of malaria. The **Golgi apparatus** is composed of a series of membranous disks called dictyosomes, each having a single lipid bilayer, that are stacked together (**[Figure 3.42](#page-138-0)**). \nEnzymes in the Golgi apparatus modify lipids and proteins transported from the ER to the Golgi, often adding carbohydrate components to them, producing glycolipids, glycoproteins, or proteoglycans. Glycolipids and glycoproteins are often inserted into the plasma membrane and are important for signal recognition by other cells or infectious particles. Different types of cells can be distinguished from one another by the structure and arrangement of the glycolipids and glycoproteins contained in their plasma membranes. These glycolipids and glycoproteins commonly also serve as cell surface receptors. \nTransport vesicles leaving the ER fuse with a Golgi apparatus on its receiving, or *cis*, face. The proteins are processed within the Golgi apparatus, and then additional transport vesicles containing the modified proteins and lipids pinch off from the Golgi apparatus on its outgoing, or *trans*, face. These outgoing vesicles move to and fuse with the plasma membrane or the membrane of other organelles. \nExocytosis is the process by which **secretory vesicles** (spherical membranous sacs) release their contents to the cell's exterior (**[Figure 3.42](#page-138-0)**). All cells have constitutive secretory pathways in which secretory vesicles transport soluble proteins that are released from the cell continually (constitutively). Certain specialized cells also have regulated secretory pathways, which are used to store soluble proteins in secretory vesicles. Regulated secretion involves substances that are only released in response to certain events or signals. For example, certain cells of the human immune system (e.g., mast cells) secrete histamine in response to the presence of foreign objects or pathogens in the body. Histamine is a compound that triggers various mechanisms used by the immune system to eliminate pathogens. \n \n**Figure 3.42** A transmission electron micrograph (left) of a Golgi apparatus in a white blood cell. The illustration (right) shows the cup-shaped, stacked disks and several transport vesicles. The Golgi apparatus modifies lipids and proteins, producing glycolipids and glycoproteins, respectively, which are commonly inserted into the plasma membrane. \n#### **Lysosomes** \nIn the 1960s, Belgian scientist Christian de Duve (1917–2013) discovered **lysosomes**, membrane-bound organelles of the endomembrane system that contain digestive enzymes. Certain types of eukaryotic cells use lysosomes to break down various particles, such as food, damaged organelles or cellular debris, microorganisms, or immune complexes. Compartmentalization of the digestive enzymes within the lysosome allows the cell to efficiently digest matter without harming the cytoplasmic components of the cell. \n \n• Name the components of the endomembrane system and describe the function of each component. \n#### **Peroxisomes** \nChristian de Duve is also credited with the discovery of **peroxisomes**, membrane-bound organelles that are not part of the endomembrane system (**[Figure 3.43](#page-139-0)**). Peroxisomes form independently in the cytoplasm from the synthesis of peroxin proteins by free ribosomes and the incorporation of these peroxin proteins into existing peroxisomes. Growing peroxisomes then divide by a process similar to binary fission. \nPeroxisomes were first named for their ability to produce hydrogen peroxide, a highly reactive molecule that helps to break down molecules such as uric acid, amino acids, and fatty acids. Peroxisomes also possess the enzyme catalase, which can degrade hydrogen peroxide. Along with the SER, peroxisomes also play a role in lipid biosynthesis. Like lysosomes, the compartmentalization of these degradative molecules within an organelle helps protect the cytoplasmic contents from unwanted damage. \nThe peroxisomes of certain organisms are specialized to meet their particular functional needs. For example, glyoxysomes are modified peroxisomes of yeasts and plant cells that perform several metabolic functions, including the production of sugar molecules. Similarly, glycosomes are modified peroxisomes made by certain trypanosomes, the pathogenic protozoans that cause Chagas disease and African sleeping sickness. \n \n**Figure 3.43** A transmission electron micrograph (left) of a cell containing a peroxisome. The illustration (right) shows the location of peroxisomes in a cell. These eukaryotic structures play a role in lipid biosynthesis and breaking down various molecules. They may also have other specialized functions depending on the cell type. (credit \"micrograph\": modification of work by American Society for Microbiology)",
"metadata": {
"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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"page_content": "Eukaryotic cells have an internal cytoskeleton made of **microfilaments**, **intermediate filaments**, and **microtubules**. This matrix of fibers and tubes provides structural support as well as a network over which materials can be transported within the cell and on which organelles can be anchored (**[Figure 3.44](#page-140-0)**). For example, the process of exocytosis involves the movement of a vesicle via the cytoskeletal network to the plasma membrane, where it can release its contents. \n \n**Figure 3.44** The cytoskeleton is a network of microfilaments, intermediate filaments, and microtubules found throughout the cytoplasm of a eukaryotic cell. In these fluorescently labeled animal cells, the microtubules are green, the actin microfilaments are red, the nucleus is blue, and keratin (a type of intermediate filament) is yellow. \nMicrofilaments are composed of two intertwined strands of actin, each composed of **actin** monomers forming filamentous cables 6 nm in diameter[25] (**[Figure 3.45](#page-141-0)**). The actin filaments work together with motor proteins, like myosin, to effect muscle contraction in animals or the amoeboid movement of some eukaryotic microbes. In ameboid organisms, actin can be found in two forms: a stiffer, polymerized, gel form and a more fluid, unpolymerized soluble form. Actin in the gel form creates stability in the ectoplasm, the gel-like area of cytoplasm just inside the plasma membrane of ameboid protozoans. \nTemporary extensions of the cytoplasmic membrane called **pseudopodia** (meaning \"false feet\") are produced through the forward flow of soluble actin filaments into the pseudopodia, followed by the gel-sol cycling of the actin filaments, resulting in cell motility. Once the cytoplasm extends outward, forming a pseudopodium, the remaining cytoplasm flows up to join the leading edge, thereby creating forward locomotion. Beyond amoeboid movement, microfilaments are also involved in a variety of other processes in eukaryotic cells, including cytoplasmic streaming (the movement or circulation of cytoplasm within the cell), cleavage furrow formation during cell division, and muscle movement in animals (**[Figure 3.45](#page-141-0)**). These functions are the result of the dynamic nature of microfilaments, which can polymerize and depolymerize relatively easily in response to cellular signals, and their interactions with molecular motors in different types of eukaryotic cells. \n25. Fuchs E, Cleveland DW. \"A Structural Scaffolding of Intermediate Filaments in Health and Disease.\" *Science* 279 no. 5350 (1998):514–519. \n \n**Figure 3.45** (a) A microfilament is composed of a pair of actin filaments. (b) Each actin filament is a string of polymerized actin monomers. (c) The dynamic nature of actin, due to its polymerization and depolymerization and its association with myosin, allows microfilaments to be involved in a variety of cellular processes, including ameboid movement, cytoplasmic streaming, contractile ring formation during cell division, and muscle contraction in animals. \nIntermediate filaments (**[Figure 3.46](#page-142-0)**) are a diverse group of cytoskeletal filaments that act as cables within the cell. They are termed \"intermediate\" because their 10-nm diameter is thicker than that of actin but thinner than that of microtubules.[26] They are composed of several strands of polymerized subunits that, in turn, are made up of a wide variety of monomers. Intermediate filaments tend to be more permanent in the cell and maintain the position of the nucleus. They also form the nuclear lamina (lining or layer) just inside the nuclear envelope. Additionally, intermediate filaments play a role in anchoring cells together in animal tissues. The intermediate filament protein desmin is found in desmosomes, the protein structures that join muscle cells together and help them resist external physical forces. The intermediate filament protein keratin is a structural protein found in hair, skin, and nails. \n26. E. Fuchs, D.W. Cleveland. \"A Structural Scaffolding of Intermediate Filaments in Health and Disease.\" *Science* 279 no. 5350 (1998):514–519. \n \n**Figure 3.46** (a) Intermediate filaments are composed of multiple strands of polymerized subunits. They are more permanent than other cytoskeletal structures and serve a variety of functions. (b) Intermediate filaments form much of the nuclear lamina. (c) Intermediate filaments form the desmosomes between cells in some animal tissues. (credit c \"illustration\": modification of work by Mariana Ruiz Villareal) \nMicrotubules (**[Figure 3.47](#page-142-1)**) are a third type of cytoskeletal fiber composed of tubulin dimers (α tubulin and β tubulin). These form hollow tubes 23 nm in diameter that are used as girders within the cytoskeleton.[27] Like microfilaments, microtubules are dynamic and have the ability to rapidly assemble and disassemble. Microtubules also work with motor proteins (such as dynein and kinesin) to move organelles and vesicles around within the cytoplasm. Additionally, microtubules are the main components of eukaryotic flagella and cilia, composing both the filament and the basal body components (**[Figure 3.54](#page-149-0)**). \n \n**Figure 3.47** (a) Microtubules are hollow structures composed of polymerized tubulin dimers. (b) They are involved in several cellular processes, including the movement of organelles throughout the cytoplasm. Motor proteins carry organelles along microtubule tracks that crisscross the entire cell. (credit b: modification of work by National Institute on Aging) \nIn addition, microtubules are involved in cell division, forming the mitotic spindle that serves to separate chromosomes during mitosis and meiosis. The mitotic spindle is produced by two **centrosomes**, which are essentially microtubule-organizing centers, at opposite ends of the cell. Each centrosome is composed of a pair of **centrioles** positioned at right angles to each other, and each centriole is an array of nine parallel microtubules arranged in triplets \n27. E. Fuchs, D.W. Cleveland. \"A Structural Scaffolding of Intermediate Filaments in Health and Disease.\" *Science* 279 no. 5350 (1998):514–519. \n#### (**[Figure 3.48](#page-143-0)**). \n \n**Figure 3.48** (a) A centrosome is composed of two centrioles positioned at right angles to each other. Each centriole is composed of nine triplets of microtubules held together by accessory proteins. (b) In animal cells, the centrosomes (arrows) serve as microtubule-organizing centers of the mitotic spindle during mitosis. \n \n• Compare and contrast the three types of cytoskeletal structures described in this section. \n#### **Mitochondria** \nThe large, complex organelles in which aerobic cellular respiration occurs in eukaryotic cells are called **mitochondria** (**[Figure 3.49](#page-144-0)**). The term \"mitochondrion\" was first coined by German microbiologist Carl Benda in 1898 and was later connected with the process of respiration by Otto Warburg in 1913. Scientists during the 1960s discovered that mitochondria have their own genome and 70S ribosomes. The mitochondrial genome was found to be bacterial, when it was sequenced in 1976. These findings ultimately supported the endosymbiotic theory proposed by Lynn Margulis, which states that mitochondria originally arose through an endosymbiotic event in which a bacterium capable of aerobic cellular respiration was taken up by phagocytosis into a host cell and remained as a viable intracellular component. \nEach mitochondrion has two lipid membranes. The outer membrane is a remnant of the original host cell's membrane structures. The inner membrane was derived from the bacterial plasma membrane. The electron transport chain for aerobic respiration uses integral proteins embedded in the inner membrane. The **mitochondrial matrix**, corresponding to the location of the original bacterium's cytoplasm, is the current location of many metabolic enzymes. It also contains mitochondrial DNA and 70S ribosomes. Invaginations of the inner membrane, called cristae, evolved to increase surface area for the location of biochemical reactions. The folding patterns of the cristae differ among various types of eukaryotic cells and are used to distinguish different eukaryotic organisms from each other. \n \n**Figure 3.49** Each mitochondrion is surrounded by two membranes, the inner of which is extensively folded into cristae and is the site of the intermembrane space. The mitochondrial matrix contains the mitochondrial DNA, ribosomes, and metabolic enzymes. The transmission electron micrograph of a mitochondrion, on the right, shows both membranes, including cristae and the mitochondrial matrix. (credit \"micrograph\": modification of work by Matthew Britton; scale-bar data from Matt Russell) \n#### **Chloroplasts** \nPlant cells and algal cells contain **chloroplasts**, the organelles in which photosynthesis occurs (**[Figure 3.50](#page-144-1)**). All chloroplasts have at least three membrane systems: the outer membrane, the inner membrane, and the thylakoid membrane system. Inside the outer and inner membranes is the chloroplast **stroma**, a gel-like fluid that makes up much of a chloroplast's volume, and in which the **thylakoid** system floats. The thylakoid system is a highly dynamic collection of folded membrane sacs. It is where the green photosynthetic pigment chlorophyll is found and the light reactions of photosynthesis occur. In most plant chloroplasts, the thylakoids are arranged in stacks called grana (singular: granum), whereas in some algal chloroplasts, the thylakoids are free floating. \n \n**Figure 3.50** Photosynthesis takes place in chloroplasts, which have an outer membrane and an inner membrane. Stacks of thylakoids called grana form a third membrane layer. \nOther organelles similar to mitochondria have arisen in other types of eukaryotes, but their roles differ. Hydrogenosomes are found in some anaerobic eukaryotes and serve as the location of anaerobic hydrogen production. Hydrogenosomes typically lack their own DNA and ribosomes. Kinetoplasts are a variation of the mitochondria found in some eukaryotic pathogens. In these organisms, each cell has a single, long, branched mitochondrion in which kinetoplast DNA, organized as multiple circular pieces of DNA, is found concentrated at one pole of the cell. \n#### **Micro Connections** \n#### **Mitochondria-Related Organelles in Protozoan Parasites** \nMany protozoans, including several protozoan parasites that cause infections in humans, can be identified by their unusual appearance. Distinguishing features may include complex cell morphologies, the presence of unique organelles, or the absence of common organelles. The protozoan parasites *Giardia lamblia* and *Trichomonas vaginalis* are two examples. \n*G. lamblia*, a frequent cause of diarrhea in humans and many other animals, is an anaerobic parasite that possesses two nuclei and several flagella. Its Golgi apparatus and endoplasmic reticulum are greatly reduced, and it lacks mitochondria completely. However, it does have organelles known as mitosomes, doublemembrane-bound organelles that appear to be severely reduced mitochondria. This has led scientists to believe that *G. lamblia'*s ancestors once possessed mitochondria that evolved to become mitosomes. *T. vaginalis*, which causes the sexually transmitted infection vaginitis, is another protozoan parasite that lacks conventional mitochondria. Instead, it possesses hydrogenosomes, mitochondrial-related, double-membranebound organelles that produce molecular hydrogen used in cellular metabolism. Scientists believe that hydrogenosomes, like mitosomes, also evolved from mitochondria.[28]",
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"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"Header 3": "**Cytoskeleton**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": "The plasma membrane of eukaryotic cells is similar in structure to the prokaryotic plasma membrane in that it is composed mainly of phospholipids forming a bilayer with embedded peripheral and integral proteins (**[Figure 3.51](#page-146-0)**). These membrane components move within the plane of the membrane according to the fluid mosaic model. However, unlike the prokaryotic membrane, eukaryotic membranes contain sterols, including cholesterol, that alter membrane fluidity. Additionally, many eukaryotic cells contain some specialized lipids, including sphingolipids, which are thought to play a role in maintaining membrane stability as well as being involved in signal transduction pathways and cell-to-cell communication. \n \n**Figure 3.51** The eukaryotic plasma membrane is composed of a lipid bilayer with many embedded or associated proteins. It contains cholesterol for the maintenance of membrane, as well as glycoproteins and glycolipids that are important in the recognition other cells or pathogens. \n#### **Membrane Transport Mechanisms** \nThe processes of simple diffusion, facilitated diffusion, and active transport are used in both eukaryotic and prokaryotic cells. However, eukaryotic cells also have the unique ability to perform various types of **endocytosis**, the uptake of matter through plasma membrane invagination and vacuole/vesicle formation (**[Figure 3.52](#page-147-0)**). A type of endocytosis involving the engulfment of large particles through membrane invagination is called **phagocytosis**, which means \"cell eating.\" In phagocytosis, particles (or other cells) are enclosed in a pocket within the membrane, which then pinches off from the membrane to form a vacuole that completely surrounds the particle. Another type of endocytosis is called **pinocytosis**, which means \"cell drinking.\" In pinocytosis, small, dissolved materials and liquids are taken into the cell through small vesicles. Saprophytic fungi, for example, obtain their nutrients from dead and decaying matter largely through pinocytosis. \n**Receptor-mediated endocytosis** is a type of endocytosis that is initiated by specific molecules called ligands when they bind to cell surface receptors on the membrane. Receptor-mediated endocytosis is the mechanism that peptide and amine-derived hormones use to enter cells and is also used by various viruses and bacteria for entry into host cells. \n \n**Figure 3.52** Three variations of endocytosis are shown. (a) In phagocytosis, the cell membrane surrounds the particle and pinches off to form an intracellular vacuole. (b) In pinocytosis, the cell membrane surrounds a small volume of fluid and pinches off, forming a vesicle. (c) In receptor-mediated endocytosis, the uptake of substances is targeted to a specific substance (a ligand) that binds at the receptor on the external cell membrane. (credit: modification of work by Mariana Ruiz Villarreal) \nThe process by which secretory vesicles release their contents to the cell's exterior is called **exocytosis**. Vesicles move toward the plasma membrane and then meld with the membrane, ejecting their contents out of the cell. Exocytosis is used by cells to remove waste products and may also be used to release chemical signals that can be taken up by other cells. \n#### **Cell Wall** \nIn addition to a plasma membrane, some eukaryotic cells have a cell wall. Cells of fungi, algae, plants, and even some protists have cell walls. Depending upon the type of eukaryotic cell, cell walls can be made of a wide range of materials, including cellulose (fungi and plants); biogenic silica, calcium carbonate, agar, and carrageenan (protists and algae); or chitin (fungi). In general, all cell walls provide structural stability for the cell and protection from environmental stresses such as desiccation, changes in osmotic pressure, and traumatic injury.[29] \n#### **Extracellular Matrix** \nCells of animals and some protozoans do not have cell walls to help maintain shape and provide structural stability. Instead, these types of eukaryotic cells produce an **extracellular matrix** for this purpose. They secrete a sticky mass of carbohydrates and proteins into the spaces between adjacent cells (**[Figure 3.53](#page-148-0)**). Some protein components assemble into a basement membrane to which the remaining extracellular matrix components adhere. Proteoglycans typically form the bulky mass of the extracellular matrix while fibrous proteins, like collagen, provide strength. Both proteoglycans and collagen are attached to fibronectin proteins, which, in turn, are attached to integrin proteins. These integrin proteins interact with transmembrane proteins in the plasma membranes of eukaryotic cells that lack cell walls. \nIn animal cells, the extracellular matrix allows cells within tissues to withstand external stresses and transmits signals from the outside of the cell to the inside. The amount of extracellular matrix is quite extensive in various types of \n29. M. Dudzick. \"Protists.\" OpenStax CNX. November 27, 2013. http://cnx.org/contents/f7048bb6-e462-459b-805c-ef291cf7049c@1 \nconnective tissues, and variations in the extracellular matrix can give different types of tissues their distinct properties. In addition, a host cell's extracellular matrix is often the site where microbial pathogens attach themselves to establish infection. For example, *Streptococcus pyogenes*, the bacterium that causes strep throat and various other infections, binds to fibronectin in the extracellular matrix of the cells lining the oropharynx (upper region of the throat). \n \n**Figure 3.53** The extracellular matrix is composed of protein and carbohydrate components. It protects cells from physical stresses and transmits signals arriving at the outside edges of the tissue to cells deeper within the tissue.",
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"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"Header 3": "**Plasma Membrane**",
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"page_content": "Some eukaryotic cells use **flagella** for locomotion; however, eukaryotic flagella are structurally distinct from those found in prokaryotic cells. Whereas the prokaryotic flagellum is a stiff, rotating structure, a eukaryotic flagellum is more like a flexible whip composed of nine parallel pairs of microtubules surrounding a central pair of microtubules. This arrangement is referred to as a 9+2 array (**[Figure 3.54](#page-149-0)**). The parallel microtubules use **dynein** motor proteins to move relative to each other, causing the flagellum to bend. \n**Cilia** (singular: **cilium**) are a similar external structure found in some eukaryotic cells. Unique to eukaryotes, cilia are shorter than flagella and often cover the entire surface of a cell; however, they are structurally similar to flagella (a 9+2 array of microtubules) and use the same mechanism for movement. A structure called a **basal body** is found at the base of each cilium and flagellum. The basal body, which attaches the cilium or flagellum to the cell, is composed of an array of triplet microtubules similar to that of a centriole but embedded in the plasma membrane. Because of their shorter length, cilia use a rapid, flexible, waving motion. In addition to motility, cilia may have other functions such as sweeping particles past or into cells. For example, ciliated protozoans use the sweeping of cilia to move food particles into their mouthparts, and ciliated cells in the mammalian respiratory tract beat in synchrony to sweep mucus \nand debris up and out of the lungs (**[Figure 3.54](#page-149-0)**). \n \n**Figure 3.54** (a) Eukaryotic flagella and cilia are composed of a 9+2 array of microtubules, as seen in this transmission electron micrograph cross-section. (b) The sliding of these microtubules relative to each other causes a flagellum to bend. (c) An illustration of *Trichomonas vaginalis*, a flagellated protozoan parasite that causes vaginitis. (d) Many protozoans, like this *Paramecium*, have numerous cilia that aid in locomotion as well as in feeding. Note the mouth opening shown here. (credit d: modification of work by University of Vermont/National Institutes of Health) \n \n- Explain how the cellular envelope of eukaryotic cells compares to that of prokaryotic cells.\n- Explain the difference between eukaryotic and prokaryotic flagella. \n#### **Clinical Focus** \n#### **Resolution** \nSince amoxicillin has not resolved Barbara's case of pneumonia, the PA prescribes another antibiotic, azithromycin, which targets bacterial ribosomes rather than peptidoglycan. After taking the azithromycin as directed, Barbara's symptoms resolve and she finally begins to feel like herself again. Presuming no drug resistance to amoxicillin was involved, and given the effectiveness of azithromycin, the causative agent of Barbara's pneumonia is most likely *Mycoplasma pneumoniae*. Even though this bacterium is a prokaryotic cell, it is not inhibited by amoxicillin because it does not have a cell wall and, therefore, does not make peptidoglycan. \n*Go back to the [previous](#page-127-0) Clinical Focus box.* \n#### **Summary** \n#### **[3.1 Spontaneous Generation](#page-99-0)** \n- The theory of **spontaneous generation** states that life arose from nonliving matter. It was a long-held belief dating back to Aristotle and the ancient Greeks.\n- Experimentation by Francesco Redi in the 17th century presented the first significant evidence refuting spontaneous generation by showing that flies must have access to meat for maggots to develop on the meat. Prominent scientists designed experiments and argued both in support of (John Needham) and against (Lazzaro Spallanzani) spontaneous generation.\n- Louis Pasteur is credited with conclusively disproving the theory of spontaneous generation with his famous swan-neck flask experiment. He subsequently proposed that \"life only comes from life.\" \n#### **[3.2 Foundations of Modern Cell Theory](#page-103-0)** \n- Although cells were first observed in the 1660s by Robert Hooke, **cell theory** was not well accepted for another 200 years. The work of scientists such as Schleiden, Schwann, Remak, and Virchow contributed to its acceptance.\n- **Endosymbiotic theory** states that mitochondria and chloroplasts, organelles found in many types of organisms, have their origins in bacteria. Significant structural and genetic information support this theory.\n- The **miasma theory of disease** was widely accepted until the 19th century, when it was replaced by the **germ theory of disease** thanks to the work of Semmelweis, Snow, Pasteur, Lister, and Koch, and others. \n#### **[3.3 Unique Characteristics of Prokaryotic Cells](#page-111-0)** \n- Prokaryotic cells differ from eukaryotic cells in that their genetic material is contained in a **nucleoid** rather than a membrane-bound nucleus. In addition, prokaryotic cells generally lack membrane-bound organelles.\n- Prokaryotic cells of the same species typically share a similar **cell morphology** and **cellular arrangement**.\n- Most prokaryotic cells have a **cell wall** that helps the organism maintain cellular morphology and protects it against changes in osmotic pressure.\n- Outside of the nucleoid, prokaryotic cells may contain extrachromosomal DNA in **plasmids**.\n- Prokaryotic **ribosomes** that are found in the cytoplasm have a size of 70S.\n- Some prokaryotic cells have **inclusions** that store nutrients or chemicals for other uses.\n- Some prokaryotic cells are able to form **endospores** through **sporulation** to survive in a dormant state when conditions are unfavorable. Endospores can **germinate**, transforming back into **vegetative cells** when conditions improve.\n- In prokaryotic cells, the **cell envelope** includes a **plasma membrane** and usually a cell wall.\n- Bacterial membranes are composed of phospholipids with integral or peripheral proteins. The fatty acid \ncomponents of these phospholipids are ester-linked and are often used to identify specific types of bacteria. The proteins serve a variety of functions, including transport, cell-to-cell communication, and sensing environmental conditions. Archaeal membranes are distinct in that they are composed of fatty acids that are ether-linked to phospholipids. \n- Some molecules can move across the bacterial membrane by simple diffusion, but most large molecules must be actively transported through membrane structures using cellular energy.\n- Prokaryotic cell walls may be composed of **peptidoglycan** (bacteria) or **pseudopeptidoglycan** (archaea).\n- Gram-positive bacterial cells are characterized by a thick **peptidoglycan** layer, whereas gram-negative bacterial cells are characterized by a thin peptidoglycan layer surrounded by an outer membrane.\n- Some prokaryotic cells produce **glycocalyx** coatings, such as **capsules** and **slime layers**, that aid in attachment to surfaces and/or evasion of the host immune system.\n- Some prokaryotic cells have **fimbriae** or **pili**, filamentous appendages that aid in attachment to surfaces. Pili are also used in the transfer of genetic material between cells.\n- Some prokaryotic cells use one or more **flagella** to move through water. **Peritrichous** bacteria, which have numerous flagella, use **runs** and **tumbles** to move purposefully in the direction of a chemical attractant. \n#### **[3.4 Unique Characteristics of Eukaryotic Cells](#page-131-0)** \n- Eukaryotic cells are defined by the presence of a **nucleus** containing the DNA genome and bound by a **nuclear membrane** (or **nuclear envelope**) composed of two lipid bilayers that regulate transport of materials into and out of the nucleus through nuclear pores.\n- Eukaryotic cell morphologies vary greatly and may be maintained by various structures, including the cytoskeleton, the cell membrane, and/or the cell wall\n- The **nucleolus**, located in the nucleus of eukaryotic cells, is the site of ribosomal synthesis and the first stages of ribosome assembly.\n- Eukaryotic cells contain **80S ribosomes** in the rough endoplasmic reticulum (**membrane bound-ribosomes**) and cytoplasm (**free ribosomes**). They contain 70s ribosomes in mitochondria and chloroplasts.\n- Eukaryotic cells have evolved an **endomembrane** system, containing membrane-bound organelles involved in transport. These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.\n- The **smooth endoplasmic reticulum** plays a role in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds. The **rough endoplasmic reticulum** contains membrane-bound 80S ribosomes that synthesize proteins destined for the cell membrane\n- The **Golgi apparatus** processes proteins and lipids, typically through the addition of sugar molecules, producing glycoproteins or glycolipids, components of the plasma membrane that are used in cell-to-cell communication.\n- **Lysosomes** contain digestive enzymes that break down small particles ingested by **endocytosis**, large particles or cells ingested by **phagocytosis**, and damaged intracellular components.\n- The **cytoskeleton**, composed of **microfilaments**, **intermediate filaments**, and **microtubules**, provides structural support in eukaryotic cells and serves as a network for transport of intracellular materials.\n- **Centrosomes** are microtubule-organizing centers important in the formation of the mitotic spindle in mitosis.\n- **Mitochondria** are the site of cellular respiration. They have two membranes: an outer membrane and an inner membrane with cristae. The mitochondrial matrix, within the inner membrane, contains the mitochondrial DNA, 70S ribosomes, and metabolic enzymes.\n- The plasma membrane of eukaryotic cells is structurally similar to that found in prokaryotic cells, and membrane components move according to the fluid mosaic model. However, eukaryotic membranes contain sterols, which alter membrane fluidity, as well as glycoproteins and glycolipids, which help the cell recognize other cells and infectious particles.\n- In addition to active transport and passive transport, eukaryotic cell membranes can take material into the cell via **endocytosis**, or expel matter from the cell via **exocytosis.** \n• Cells of fungi, algae, plants, and some protists have a **cell wall,** whereas cells of animals and some protozoans have a sticky **extracellular matrix** that provides structural support and mediates cellular signaling. \n• Eukaryotic flagella are structurally distinct from prokaryotic flagella but serve a similar purpose (locomotion). **Cilia** are structurally similar to eukaryotic flagella, but shorter; they may be used for locomotion, feeding, or movement of extracellular particles.",
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"Header 2": "**Flagella and Cilia**",
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"page_content": "#### **Multiple Choice** \n- **1.** Which of the following individuals argued in favor of the theory of spontaneous generation?\n- a. Francesco Redi\n- b. Louis Pasteur\n- c. John Needham\n- d. Lazzaro Spallanzani\n- **2.** Which of the following individuals is credited for definitively refuting the theory of spontaneous generation using broth in swan-neck flask?\n- a. Aristotle\n- b. Jan Baptista van Helmont\n- c. John Needham\n- d. Louis Pasteur\n- **3.** Which of the following experimented with raw meat, maggots, and flies in an attempt to disprove the theory of spontaneous generation.\n- a. Aristotle\n- b. Lazzaro Spallanzani\n- c. Antonie van Leeuwenhoek\n- d. Francesco Redi\n- **4.** Which of the following individuals did not contribute to the establishment of cell theory?\n- a. Girolamo Fracastoro\n- b. Matthias Schleiden\n- c. Robert Remak\n- d. Robert Hooke\n- **5.** Whose proposal of the endosymbiotic theory of mitochondrial and chloroplast origin was ultimately accepted by the greater scientific community?\n- a. Rudolf Virchow\n- b. Ignaz Semmelweis\n- c. Lynn Margulis\n- d. Theodor Schwann \n- **6.** Which of the following developed a set of postulates for determining whether a particular disease is caused by a particular pathogen?\n- a. John Snow\n- b. Robert Koch\n- c. Joseph Lister\n- d. Louis Pasteur\n- **7.** Which of the following terms refers to a prokaryotic cell that is comma shaped?\n- a. coccus\n- b. coccobacilli\n- c. vibrio\n- d. spirillum\n- **8.** Which bacterial structures are important for adherence to surfaces? (Select all that apply.)\n- a. endospores\n- b. cell walls\n- c. fimbriae\n- d. capsules\n- e. flagella\n- **9.** Which of the following cell wall components is unique to gram-negative cells?\n- a. lipopolysaccharide\n- b. teichoic acid\n- c. mycolic acid\n- d. peptidoglycan\n- **10.** Which of the following terms refers to a bacterial cell having a single tuft of flagella at one end?\n- a. monotrichous\n- b. amphitrichous\n- c. peritrichous\n- d. lophotrichous\n- **11.** Bacterial cell walls are primarily composed of which of the following?\n- a. phospholipid\n- b. protein\n- c. carbohydrate\n- d. peptidoglycan \n- **12.** Which of the following organelles is not part of the endomembrane system?\n- a. endoplasmic reticulum\n- b. Golgi apparatus\n- c. lysosome\n- d. peroxisome\n- **13.** Which type of cytoskeletal fiber is important in the formation of the nuclear lamina?\n- a. microfilaments\n- b. intermediate filaments\n- c. microtubules\n- d. fibronectin\n- **14.** Sugar groups may be added to proteins in which of the following?\n- a. smooth endoplasmic reticulum\n- b. rough endoplasmic reticulum\n- c. Golgi apparatus\n- d. lysosome\n- **15.** Which of the following structures of a eukaryotic cell is not likely derived from endosymbiotic bacterium?\n- a. mitochondrial DNA\n- b. mitochondrial ribosomes\n- c. inner membrane\n- d. outer membrane\n- **16.** Which type of nutrient uptake involves the engulfment of small dissolved molecules into vesicles?\n- a. active transport\n- b. pinocytosis\n- c. receptor-mediated endocytosis\n- d. facilitated diffusion\n- **17.** Which of the following is not composed of microtubules?\n- a. desmosomes\n- b. centrioles\n- c. eukaryotic flagella\n- d. eukaryotic cilia \n#### **True/False** \n- **18.** Exposure to air is necessary for microbial growth.\n- **19.** Bacteria have 80S ribosomes each composed of a 60S large subunit and a 40S small subunit.\n- **20.** Mitochondria in eukaryotic cells contain ribosomes that are structurally similar to those found in prokaryotic cells. \n#### **Fill in the Blank** \n| 21. | The assertion that \"life only comes from life\" was stated by Louis Pasteur in regard to his experiments that
definitively refuted the theory of | | | |\n|-----|----------------------------------------------------------------------------------------------------------------------------------------------------|--|--|--|\n| 22. | John Snow is known as the Father of | | | |\n| 23. | The theory states that disease may originate from proximity to decomposing matter and is not
due to person-to-person contact. | | | |\n| 24. | The scientist who first described cells was | | | |\n| 25. | Prokaryotic cells that are rod-shaped are called | | | |\n| 26. | The type of inclusion containing polymerized inorganic phosphate is called | | | |\n| 27. | Peroxisomes typically produce, a harsh chemical that helps break down molecules. | | | |\n| 28. | Microfilaments are composed of monomers. | | | |\n| | | | | | \n#### **Short Answer** \n- **29.** Explain in your own words Pasteur's swan-neck flask experiment.\n- **30.** Explain why the experiments of Needham and Spallanzani yielded in different results even though they used similar methodologies.\n- **31.** How did the explanation of Virchow and Remak for the origin of cells differ from that of Schleiden and Schwann?\n- **32.** What evidence exists that supports the endosymbiotic theory?\n- **33.** What were the differences in mortality rates due to puerperal fever that Ignaz Semmelweis observed? How did he propose to reduce the occurrence of puerperal fever? Did it work?\n- **34.** What is the direction of water flow for a bacterial cell living in a hypotonic environment? How do cell walls help bacteria living in such environments?\n- **35.** How do bacterial flagella respond to a chemical gradient of an attractant to move toward a higher concentration of the chemical? \n**36.** Label the parts of the prokaryotic cell. \n \n- **37.** What existing evidence supports the theory that mitochondria are of prokaryotic origin?\n- **38.** Why do eukaryotic cells require an endomembrane system?\n- **39.** Name at least two ways that prokaryotic flagella are different from eukaryotic flagella. \n#### **Critical Thinking** \n- **40.** What would the results of Pasteur's swan-neck flask experiment have looked like if they supported the theory of spontaneous generation?\n- **41.** Why are mitochondria and chloroplasts unable to multiply outside of a host cell?\n- **42.** Why was the work of Snow so important in supporting the germ theory?\n- **43.** Which of the following slides is a good example of staphylococci? \n \n**Figure 3.55** (credit a: modification of work by U.S. Department of Agriculture; credit b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by NIAID) \n- **44.** Provide some examples of bacterial structures that might be used as antibiotic targets and explain why.\n- **45.** The causative agent of botulism, a deadly form of food poisoning, is an endospore-forming bacterium called *Clostridium botulinim*. Why might it be difficult to kill this bacterium in contaminated food? \n**46.** Label the lettered parts of this eukaryotic cell. \n \n**47.** How are peroxisomes more like mitochondria than like the membrane-bound organelles of the endomembrane system? How do they differ from mitochondria? \n**48.** Why must the functions of both lysosomes and peroxisomes be compartmentalized?",
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"Header 2": "**Flagella and Cilia**",
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"page_content": "#### **Learning Objectives** \n- Identify and describe unique examples of prokaryotes in various habitats on earth\n- Identify and describe symbiotic relationships\n- Compare normal/commensal/resident microbiota to transient microbiota\n- Explain how prokaryotes are classified \nAll living organisms are classified into three domains of life: Archaea, Bacteria, and Eukarya. In this chapter, we will focus on the domains Archaea and Bacteria. Archaea and bacteria are unicellular prokaryotic organisms. Unlike eukaryotes, they have no nuclei or any other membrane-bound organelles.\n\nProkaryotes are ubiquitous. They can be found everywhere on our planet, even in hot springs, in the Antarctic ice shield, and under extreme pressure two miles under water. One bacterium, *Paracoccus denitrificans*, has even been shown to survive when scientists removed it from its native environment (soil) and used a centrifuge to subject it to forces of gravity as strong as those found on the surface of Jupiter. \nProkaryotes also are abundant on and within the human body. According to a report by National Institutes of Health, prokaryotes, especially bacteria, outnumber human cells 10:1.[1] More recent studies suggest the ratio could be closer to 1:1, but even that ratio means that there are a great number of bacteria within the human body.[2] Bacteria thrive in the human mouth, nasal cavity, throat, ears, gastrointestinal tract, and vagina. Large colonies of bacteria can be found on healthy human skin, especially in moist areas (armpits, navel, and areas behind ears). However, even drier areas of the skin are not free from bacteria. \n#### **Clinical Focus** \n#### **Part 1** \nMarsha, a 20-year-old university student, recently returned to the United States from a trip to Nigeria, where she had interned as a medical assistant for an organization working to improve access to laboratory services for tuberculosis testing. When she returned, Marsha began to feel fatigue, which she initially attributed to jet lag. However, the fatigue persisted, and Marsha soon began to experience other bothersome symptoms, such as occasional coughing, night sweats, loss of appetite, and a low-grade fever of 37.4 °C (99.3 °F). \nMarsha expected her symptoms would subside in a few days, but instead, they gradually became more severe. About two weeks after returning home, she coughed up some sputum and noticed that it contained blood and small whitish clumps resembling cottage cheese. Her fever spiked to 38.2 °C (100.8 °F), and she began feeling sharp pains in her chest when breathing deeply. Concerned that she seemed to be getting worse, Marsha scheduled an appointment with her physician. \n• Could Marsha's symptoms be related to her overseas travel, even several weeks after returning home? \n*Jump to the [next](#page-170-0) Clinical Focus box.* \n1. Medical Press. \"Mouth Bacteria Can Change Their Diet, Supercomputers Reveal.\" August 12, 2014. http://medicalxpress.com/news/ 2014-08-mouth-bacteria-diet-supercomputers-reveal.html. Accessed February 24, 2015. \n2. A. Abbott. \"Scientists Bust Myth That Our Bodies Have More Bacteria Than Human Cells: Decades-Old Assumption about Microbiota Revisited.\" *Nature.* http://www.nature.com/news/scientists-bust-myth-that-our-bodies-have-more-bacteria-than-human-cells-1.19136. Accessed June 3, 2016. \nChapter 4 | Prokaryotic Diversity 151 \nThe existence of prokaryotes is very important for the stability and thriving of ecosystems. For example, they are a necessary part of soil formation and stabilization processes through the breakdown of organic matter and development of biofilms. One gram of soil contains up to 10 billion microorganisms (most of them prokaryotic) belonging to about 1,000 species. Many species of bacteria use substances released from plant roots, such as acids and carbohydrates, as nutrients. The bacteria metabolize these plant substances and release the products of bacterial metabolism back to the soil, forming humus and thus increasing the soil's fertility. In salty lakes such as the Dead Sea (**[Figure 4.2](#page-160-0)**), salt-loving halobacteria decompose dead brine shrimp and nourish young brine shrimp and flies with the products of bacterial metabolism. \n \n \n**Figure 4.2** (a) Some prokaryotes, called halophiles, can thrive in extremely salty environments such as the Dead Sea, pictured here. (b) The archaeon *Halobacterium salinarum*, shown here in an electron micrograph, is a halophile that lives in the Dead Sea. (credit a: modification of work by Jullen Menichini; credit b: modification of work by NASA) \nIn addition to living in the ground and the water, prokaryotic microorganisms are abundant in the air, even high in the atmosphere. There may be up to 2,000 different kinds of bacteria in the air, similar to their diversity in the soil. \nProkaryotes can be found everywhere on earth because they are extremely resilient and adaptable. They are often metabolically flexible, which means that they might easily switch from one energy source to another, depending on the availability of the sources, or from one metabolic pathway to another. For example, certain prokaryotic cyanobacteria can switch from a conventional type of lipid metabolism, which includes production of fatty aldehydes, to a different type of lipid metabolism that generates biofuel, such as fatty acids and wax esters. Groundwater bacteria store complex high-energy carbohydrates when grown in pure groundwater, but they metabolize these molecules when the groundwater is enriched with phosphates. Some bacteria get their energy by reducing sulfates into sulfides, but can switch to a different metabolic pathway when necessary, producing acids and free hydrogen ions. \nProkaryotes perform functions vital to life on earth by capturing (or \"fixing\") and recycling elements like carbon and nitrogen. Organisms such as animals require organic carbon to grow, but, unlike prokaryotes, they are unable to use inorganic carbon sources like carbon dioxide. Thus, animals rely on prokaryotes to convert carbon dioxide into organic carbon products that they can use. This process of converting carbon dioxide to organic carbon products is called carbon fixation. \nPlants and animals also rely heavily on prokaryotes for nitrogen fixation, the conversion of atmospheric nitrogen into ammonia, a compound that some plants can use to form many different biomolecules necessary to their survival. Bacteria in the genus *Rhizobium*, for example, are nitrogen-fixing bacteria; they live in the roots of legume plants such as clover, alfalfa, and peas (**[Figure 4.3](#page-161-0)**). Ammonia produced by *Rhizobium* helps these plants to survive by enabling them to make building blocks of nucleic acids. In turn, these plants may be eaten by animals—sustaining their growth and survival—or they may die, in which case the products of nitrogen fixation will enrich the soil and be used by other plants. \n \n**Figure 4.3** (a) Nitrogen-fixing bacteria such as *Rhizobium* live in the root nodules of legumes such as clover. (b) This micrograph of the root nodule shows bacteroids (bacterium-like cells or modified bacterial cells) within the plant cells. The bacteroids are visible as darker ovals within the larger plant cell. (credit a: modification of work by USDA) \nAnother positive function of prokaryotes is in cleaning up the environment. Recently, some researchers focused on the diversity and functions of prokaryotes in manmade environments. They found that some bacteria play a unique role in degrading toxic chemicals that pollute water and soil.[3] \nDespite all of the positive and helpful roles prokaryotes play, some are human pathogens that may cause illness or infection when they enter the body. In addition, some bacteria can contaminate food, causing spoilage or foodborne illness, which makes them subjects of concern in food preparation and safety. Less than 1% of prokaryotes (all of them bacteria) are thought to be human pathogens, but collectively these species are responsible for a large number of the diseases that afflict humans. \nBesides pathogens, which have a direct impact on human health, prokaryotes also affect humans in many indirect ways. For example, prokaryotes are now thought to be key players in the processes of climate change. In recent years, as temperatures in the earth's polar regions have risen, soil that was formerly frozen year-round (permafrost) has begun to thaw. Carbon trapped in the permafrost is gradually released and metabolized by prokaryotes. This produces massive amounts of carbon dioxide and methane, greenhouse gases that escape into the atmosphere and contribute to the greenhouse effect. \n \n- In what types of environments can prokaryotes be found?\n- Name some ways that plants and animals rely on prokaryotes.\n\nAs we have learned, prokaryotic microorganisms can associate with plants and animals. Often, this association results in unique relationships between organisms. For example, bacteria living on the roots or leaves of a plant get nutrients from the plant and, in return, produce substances that protect the plant from pathogens. On the other hand, some bacteria are plant pathogens that use mechanisms of infection similar to bacterial pathogens of animals and humans. \nProkaryotes live in a **community**, or a group of interacting populations of organisms. A population is a group of individual organisms belonging to the same biological species and limited to a certain geographic area. Populations \n3. A.M. Kravetz \"Unique Bacteria Fights Man-Made Chemical Waste.\" 2012. http://www.livescience.com/25181-bacteria-strain-cleans-uptoxins-nsf-bts.html. Accessed March 9, 2015. \ncan have **cooperative interactions**, which benefit the populations, or **competitive interactions**, in which one population competes with another for resources. The study of these interactions between populations is called **microbial ecology**. \nAny interaction between different species within a community is called **symbiosis**. Such interactions fall along a continuum between opposition and cooperation. Interactions in a symbiotic relationship may be beneficial or harmful, or have no effect on one or both of the species involved. **[Table 4.1](#page-162-0)** summarizes the main types of symbiotic interactions among prokaryotes. \n| Type | Population A | Population B |\n|--------------|--------------|--------------|\n| Mutualism | Benefitted | Benefitted |\n| Amensalism | Harmed | Unaffected |\n| Commensalism | Benefitted | Unaffected |\n| Neutralism | Unaffected | Unaffected |\n| Parasitism | Benefitted | Harmed | \n**Types of Symbiotic Relationships** \n**Table 4.1** \nWhen two species benefit from each other, the symbiosis is called **mutualism** (or syntropy, or crossfeeding). For example, humans have a mutualistic relationship with the bacterium *Bacteroides thetaiotetraiotamicron*, which lives in the intestinal tract. *B. thetaiotetraiotamicron* digests complex polysaccharide plant materials that human digestive enzymes cannot break down, converting them into monosaccharides that can be absorbed by human cells. Humans also have a mutualistic relationship with certain strains of *Escherichia coli*, another bacterium found in the gut. *E. coli* relies on intestinal contents for nutrients, and humans derive certain vitamins from *E. coli,* particularly vitamin K, which is required for the formation of blood clotting factors. (This is only true for some strains of *E. coli*, however. Other strains are pathogenic and do not have a mutualistic relationship with humans.) \nA type of symbiosis in which one population harms another but remains unaffected itself is called **amensalism**. In the case of bacteria, some amensalist species produce bactericidal substances that kill other species of bacteria. For example, the bacterium *Lucilia sericata* produces a protein that destroys *Staphylococcus aureus*, a bacterium commonly found on the surface of the human skin. Too much handwashing can affect this relationship and lead to *S. aureus* diseases and transmission. \nIn another type of symbiosis, called **commensalism**, one organism benefits while the other is unaffected. This occurs when the bacterium *Staphylococcus epidermidis* uses the dead cells of the human skin as nutrients. Billions of these bacteria live on our skin, but in most cases (especially when our immune system is healthy), we do not react to them in any way. \nIf neither of the symbiotic organisms is affected in any way, we call this type of symbiosis **neutralism**. An example of neutralism is the coexistence of metabolically active (vegetating) bacteria and endospores (dormant, metabolically passive bacteria). For example, the bacterium *Bacillus anthracis* typically forms endospores in soil when conditions are unfavorable. If the soil is warmed and enriched with nutrients, some endospores germinate and remain in symbiosis with other endospores that have not germinated. \nA type of symbiosis in which one organism benefits while harming the other is called **parasitism**. The relationship between humans and many pathogenic prokaryotes can be characterized as parasitic because these organisms invade the body, producing toxic substances or infectious diseases that cause harm. Diseases such as tetanus, diphtheria, pertussis, tuberculosis, and leprosy all arise from interactions between bacteria and humans. \nScientists have coined the term **microbiome** to refer to all prokaryotic and eukaryotic microorganisms that are associated with a certain organism. Within the human microbiome, there are **resident microbiota** and **transient** **microbiota**. The resident microbiota consists of microorganisms that constantly live in or on our bodies. The term transient microbiota refers to microorganisms that are only temporarily found in the human body, and these may include pathogenic microorganisms. Hygiene and diet can alter both the resident and transient microbiota. \nThe resident microbiota is amazingly diverse, not only in terms of the variety of species but also in terms of the preference of different microorganisms for different areas of the human body. For example, in the human mouth, there are thousands of commensal or mutualistic species of bacteria. Some of these bacteria prefer to inhabit the surface of the tongue, whereas others prefer the internal surface of the cheeks, and yet others prefer the front or back teeth or gums. The inner surface of the cheek has the least diverse microbiota because of its exposure to oxygen. By contrast, the crypts of the tongue and the spaces between teeth are two sites with limited oxygen exposure, so these sites have more diverse microbiota, including bacteria living in the absence of oxygen (e.g., *Bacteroides*, *Fusobacterium*). Differences in the oral microbiota between randomly chosen human individuals are also significant. Studies have shown, for example, that the prevalence of such bacteria as *Streptococcus*, *Haemophilus*, *Neisseria*, and others was dramatically different when compared between individuals.[4] \nThere are also significant differences between the microbiota of different sites of the same human body. The inner surface of the cheek has a predominance of *Streptococcus*, whereas in the throat, the palatine tonsil, and saliva, there are two to three times fewer *Streptococcus*, and several times more *Fusobacterium*. In the plaque removed from gums, the predominant bacteria belong to the genus *Fusobacterium.* However, in the intestine, both *Streptococcus* and *Fusobacterium* disappear, and the genus *Bacteroides* becomes predominant. \nNot only can the microbiota vary from one body site to another, the microbiome can also change over time within the same individual. Humans acquire their first inoculations of normal flora during natural birth and shortly after birth. Before birth, there is a rapid increase in the population of *Lactobacillus* spp. in the vagina, and this population serves as the first colonization of microbiota during natural birth. After birth, additional microbes are acquired from healthcare providers, parents, other relatives, and individuals who come in contact with the baby. This process establishes a microbiome that will continue to evolve over the course of the individual's life as new microbes colonize and are eliminated from the body. For example, it is estimated that within a 9-hour period, the microbiota of the small intestine can change so that half of the microbial inhabitants will be different.[5] The importance of the initial *Lactobacillus* colonization during vaginal child birth is highlighted by studies demonstrating a higher incidence of diseases in individuals born by cesarean section, compared to those born vaginally. Studies have shown that babies born vaginally are predominantly colonized by vaginal lactobacillus, whereas babies born by cesarean section are more frequently colonized by microbes of the normal skin microbiota, including common hospital-acquired pathogens. \nThroughout the body, resident microbiotas are important for human health because they occupy niches that might be otherwise taken by pathogenic microorganisms. For instance, *Lactobacillus* spp. are the dominant bacterial species of the normal vaginal microbiota for most women. lactobacillus produce lactic acid, contributing to the acidity of the vagina and inhibiting the growth of pathogenic yeasts. However, when the population of the resident microbiota is decreased for some reason (e.g., because of taking antibiotics), the pH of the vagina increases, making it a more favorable environment for the growth of yeasts such as *Candida albicans*. Antibiotic therapy can also disrupt the microbiota of the intestinal tract and respiratory tract, increasing the risk for secondary infections and/or promoting the long-term carriage and shedding of pathogens. \n \n- Explain the difference between cooperative and competitive interactions in microbial communities.\n- List the types of symbiosis and explain how each population is affected. \n4. E.M. Bik et al. \"Bacterial Diversity in the Oral Cavity of 10 Healthy Individuals.\" *The ISME Journal* 4 no. 8 (2010):962–974. \n5. C.C. Booijink et al. \"High Temporal and Intra-Individual Variation Detected in the Human Ileal Microbiota.\" *Environmental Microbiology* 12 no. 12 (2010):3213–3227.",
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"page_content": "#### **Learning Objectives** \n- Describe the unique features of each class within the phylum Proteobacteria: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria\n- Give an example of a bacterium in each class of Proteobacteria \nIn 1987, the American microbiologist Carl Woese (1928–2012) suggested that a large and diverse group of bacteria that he called \"purple bacteria and their relatives\" should be defined as a separate phylum within the domain Bacteria based on the similarity of the nucleotide sequences in their genome.[10] This phylum of gram-negative bacteria subsequently received the name **Proteobacteria**. It includes many bacteria that are part of the normal human microbiota as well as many pathogens. The Proteobacteria are further divided into five classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria (**[Appendix D](#page-1244-0)**).\n\nThe first class of Proteobacteria is the **Alphaproteobacteria**. The unifying characteristic of this class is that they are **oligotroph**s, organisms capable of living in low-nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil. \nAmong the Alphaproteobacteria are two taxa, chlamydias and rickettsias, that are **obligate intracellular pathogen**s, meaning that part of their life cycle must occur inside other cells called host cells. When not growing inside a host cell, *Chlamydia* and *Rickettsia* are metabolically inactive outside of the host cell. They cannot synthesize their own adenosine triphosphate (ATP), and, therefore, rely on cells for their energy needs. \n*Rickettsia* spp. include a number of serious human pathogens. For example, *R. rickettsii* causes Rocky Mountain spotted fever, a life-threatening form of meningoencephalitis (inflammation of the membranes that wrap the brain). *R. rickettsii* infects ticks and can be transmitted to humans via a bite from an infected tick (**[Figure 4.4](#page-166-1)**). \n \n**Figure 4.4** Rickettsias require special staining methods to see them under a microscope. Here, *R. rickettsii*, which causes Rocky Mountain spotted fever, is shown infecting the cells of a tick. (credit: modification of work by Centers for Disease Control and Prevention) \nAnother species of *Rickettsia*, *R. prowazekii*, is spread by lice. It causes epidemic typhus, a severe infectious disease common during warfare and mass migrations of people. *R. prowazekii* infects human endothelium cells, causing inflammation of the inner lining of blood vessels, high fever, abdominal pain, and sometimes delirium. A relative, *R. typhi*, causes a less severe disease known as murine or endemic typhus, which is still observed in the southwestern United States during warm seasons. \n*Chlamydia* is another taxon of the Alphaproteobacteria. Members of this genus are extremely resistant to the cellular defenses, giving them the ability to spread from host to host rapidly via elementary bodies. The metabolically and reproductively inactive **elementary bodies** are the endospore-like form of intracellular bacteria that enter an epithelial cell, where they become active. **[Figure 4.5](#page-167-0)** illustrates the life cycle of *Chlamydia*. \n*C. trachomatis* is a human pathogen that causes trachoma, a disease of the eyes, often leading to blindness. *C. trachomatis* also causes the sexually transmitted disease lymphogranuloma venereum (LGV). This disease is often mildly symptomatic, manifesting as regional lymph node swelling, or it may be asymptomatic, but it is extremely contagious and is common on college campuses. \n**[Table 4.2](#page-168-0)** summarizes the characteristics of important genera of Alphaproteobacteria. \n \n**Figure 4.5** *Chlamydia* begins infection of a host when the metabolically inactive elementary bodies enter an epithelial cell. Once inside the host cell, the elementary bodies turn into active reticulate bodies. The reticulate bodies multiply and release more elementary bodies when the cell dies after the *Chlamydia* uses all of the host cell's ATP. (credit: modification of work by Centers for Disease Control and Prevention) \nChapter 4 | Prokaryotic Diversity 159 \n#### **Class Alphaproteobacteria** \n| Genus | Microscopic
Morphology | Unique Characteristics |\n|----------------|--------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| Agrobacterium | Gram-negative bacillus | Plant pathogen; one species, A. tumefaciens, causes tumors in
plants |\n| Bartonella | Gram-negative,
pleomorphic, flagellated
coccobacillus | Facultative intracellular bacteria, transmitted by lice and fleas,
cause trench fever and cat scratch disease in humans |\n| Brucella | Gram-negative, small,
flagellated coccobacillus | Facultative intracellular bacteria, transmitted by contaminated
milk from infected cows, cause brucellosis in cattle and
humans |\n| Caulobacter | Gram-negative bacillus | Used in studies on cellular adaptation and differentiation
because of its peculiar life cycle (during cell division, forms
\"swarm\" cells and \"stalked\" cells) |\n| Chlamydia | Gram-negative, coccoid
or ovoid bacterium | Obligatory intracellular bacteria; some cause chlamydia,
trachoma, and pneumonia |\n| Coxiella | Small, gram-negative
bacillus | Obligatory intracellular bacteria; cause Q fever; potential for
use as biological weapon |\n| Ehrlichia | Very small, gram
negative, coccoid or
ovoid bacteria | Obligatory intracellular bacteria; can be transported from cell to
cell; transmitted by ticks; cause ehrlichiosis (destruction of
white blood cells and inflammation) in humans and dogs |\n| Hyphomicrobium | Gram-negative bacilli;
grows from a stalk | Similar to Caulobacter |\n| Methylocystis | Gram-negative, coccoid
or short bacilli | Nitrogen-fixing aerobic bacteria |\n| Rhizobium | Gram-negative,
rectangular bacilli with
rounded ends forming
clusters | Nitrogen-fixing bacteria that live in soil and form symbiotic
relationship with roots of legumes (e.g., clover, alfalfa, and
beans) |\n| Rickettsia | Gram-negative, highly
pleomorphic bacteria
(may be cocci, rods, or
threads) | Obligate intracellular bacteria; transmitted by ticks; may cause
Rocky Mountain spotted fever and typhus | \n**Table 4.2** \n \n• What characteristic do all Alphaproteobacteria share?\n\nUnlike Alphaproteobacteria, which survive on a minimal amount of nutrients, the class **Betaproteobacteria** are **eutroph**s (or copiotrophs), meaning that they require a copious amount of organic nutrients. Betaproteobacteria often grow between aerobic and anaerobic areas (e.g., in mammalian intestines). Some genera include species that are human pathogens, able to cause severe, sometimes life-threatening disease. The genus *Neisseria*, for example, includes the bacteria *N. gonorrhoeae,* the causative agent of the STI gonorrhea, and *N. meningitides*, the causative agent of bacterial meningitis. \n*Neisseria* are cocci that live on mucosal surfaces of the human body. They are fastidious, or difficult to culture, and they require high levels of moisture, nutrient supplements, and carbon dioxide. Also, *Neisseria* are microaerophilic, meaning that they require low levels of oxygen. For optimal growth and for the purposes of identification, *Neisseria* spp. are grown on chocolate agar (i.e., agar supplemented by partially hemolyzed red blood cells). Their characteristic pattern of growth in culture is diplococcal: pairs of cells resembling coffee beans (**[Figure 4.6](#page-169-0)**). \n \n**Figure 4.6** *Neisseria meningitidis* growing in colonies on a chocolate agar plate. (credit: Centers for Disease Control and Prevention) \nThe pathogen responsible for pertussis (whooping cough) is also a member of Betaproteobacteria. The bacterium *Bordetella pertussis*, from the order Burkholderiales, produces several toxins that paralyze the movement of cilia in the human respiratory tract and directly damage cells of the respiratory tract, causing a severe cough. \n**[Table 4.3](#page-169-1)** summarizes the characteristics of important genera of Betaproteobacteria. \n#### **Example Genus Microscopic Morphology Unique Characteristics** *Bordetella* A small, gram-negative coccobacillus Aerobic, very fastidious; *B. pertussis* causes pertussis (whooping cough) *Burkholderia* Gram-negative bacillus Aerobic, aquatic, cause diseases in horses and humans (especially patients with cystic fibrosis); agents of nosocomial infections *Leptothrix* Gram-negative, sheathed, filamentous bacillus Aquatic; oxidize iron and manganese; can live in wastewater treatment plants and clog pipes *Neisseria* Gram-negative, coffee bean-shaped coccus forming pairs Require moisture and high concentration of carbon dioxide; oxidase positive, grow on chocolate agar; pathogenic species cause gonorrhea and meningitis \n*Thiobacillus* Gram-negative bacillus Thermophilic, acidophilic, strictly aerobic bacteria; oxidize iron and \nsulfur \n**Class Betaproteobacteria** \n**Table 4.3** \n \n• What characteristic do all Betaproteobacteria share? \n#### **Clinical Focus** \n#### **Part 2** \nWhen Marsha finally went to the doctor's office, the physician listened to her breathing through a stethoscope. He heard some crepitation (a crackling sound) in her lungs, so he ordered a chest radiograph and asked the nurse to collect a sputum sample for microbiological evaluation and cytology. The radiologic evaluation found cavities, opacities, and a particular pattern of distribution of abnormal material (**[Figure 4.7](#page-170-1)**). \n• What are some possible diseases that could be responsible for Marsha's radiograph results? \n \n**Figure 4.7** This anteroposterior radiograph shows the presence of bilateral pulmonary infiltrate (white triangles) and \"caving formation\" (black arrows) present in the right apical region. (credit: Centers for Disease Control and Prevention) \n*Jump to the [next](#page-185-0) Clinical Focus box. Go back to the [previous](#page-159-1) Clinical Focus box.*\n\nThe most diverse class of gram-negative bacteria is **Gammaproteobacteria**, and it includes a number of human pathogens. For example, a large and diverse family, *Pseudomonaceae*, includes the genus *Pseudomonas*. Within this genus is the species *P. aeruginosa*, a pathogen responsible for diverse infections in various regions of the body. *P. aeruginosa* is a strictly aerobic, nonfermenting, highly motile bacterium. It often infects wounds and burns, can be the cause of chronic urinary tract infections, and can be an important cause of respiratory infections in patients with cystic fibrosis or patients on mechanical ventilators. Infections by *P. aeruginosa* are often difficult to treat because the bacterium is resistant to many antibiotics and has a remarkable ability to form biofilms. Other representatives of *Pseudomonas* include the fluorescent (glowing) bacterium *P. fluorescens* and the soil bacteria *P. putida*, which is known for its ability to degrade xenobiotics (substances not naturally produced or found in living organisms). \nThe *Pasteurellaceae* also includes several clinically relevant genera and species. This family includes several bacteria that are human and/or animal pathogens. For example, *Pasteurella haemolytica* causes severe pneumonia in sheep and goats. *P. multocida* is a species that can be transmitted from animals to humans through bites, causing infections of the skin and deeper tissues. The genus *Haemophilus* contains two human pathogens, *H. influenzae* and *H. ducreyi*. Despite its name, *H. influenzae* does not cause influenza (which is a viral disease). *H. influenzae* can cause both upper and lower respiratory tract infections, including sinusitis, bronchitis, ear infections, and pneumonia. Before the development of effective vaccination, strains of *H. influenzae* were a leading cause of more invasive diseases, like meningitis in children. *H. ducreyi* causes the STI known as chancroid. \nThe order Vibrionales includes the human pathogen *Vibrio cholerae*. This comma-shaped aquatic bacterium thrives \nin highly alkaline environments like shallow lagoons and sea ports. A toxin produced by *V. cholerae* causes hypersecretion of electrolytes and water in the large intestine, leading to profuse watery diarrhea and dehydration. *V. parahaemolyticus* is also a cause of gastrointestinal disease in humans, whereas *V. vulnificus* causes serious and potentially life-threatening cellulitis (infection of the skin and deeper tissues) and blood-borne infections. Another representative of Vibrionales, *Aliivibrio fischeri*, engages in a symbiotic relationship with squid. The squid provides nutrients for the bacteria to grow and the bacteria produce bioluminescence that protects the squid from predators (**[Figure 4.8](#page-171-0)**). \n \n**Figure 4.8** (a) *Aliivibrio fischeri* is a bioluminescent bacterium. (b) *A. fischeri* colonizes and lives in a mutualistic relationship with the Hawaiian bobtail squid (*Euprymna scolopes*). (credit a: modification of work by American Society for Microbiology; credit b: modification of work by Margaret McFall-Ngai) \nThe genus *Legionella* also belongs to the Gammaproteobacteria. *L. pneumophila,* the pathogen responsible for Legionnaires disease, is an aquatic bacterium that tends to inhabit pools of warm water, such as those found in the tanks of air conditioning units in large buildings (**[Figure 4.9](#page-171-1)**). Because the bacteria can spread in aerosols, outbreaks of Legionnaires disease often affect residents of a building in which the water has become contaminated with *Legionella.* In fact, these bacteria derive their name from the first known outbreak of Legionnaires disease, which occurred in a hotel hosting an American Legion veterans' association convention in Philadelphia in 1976. \n \n \n**Figure 4.9** (a) *Legionella pneumophila*, the causative agent of Legionnaires disease, thrives in warm water. (b) Outbreaks of Legionnaires disease often originate in the air conditioning units of large buildings when water in or near the system becomes contaminated with *L. pneumophila.* (credit a: modification of work by Centers for Disease Control and Prevention) \nEnterobacteriaceae is a large family of **enteric** (intestinal) bacteria belonging to the Gammaproteobacteria. They are facultative anaerobes and are able to ferment carbohydrates. Within this family, microbiologists recognize two distinct categories. The first category is called the coliforms, after its prototypical bacterium species, *Escherichia coli*. Coliforms are able to ferment lactose completely (i.e., with the production of acid and gas). The second category, noncoliforms, either cannot ferment lactose or can only ferment it incompletely (producing either acid or gas, but not both). The noncoliforms include some notable human pathogens, such as *Salmonella* spp*., Shigella* spp*.,* and *Yersinia pestis*. \n*E. coli* has been perhaps the most studied bacterium since it was first described in 1886 by Theodor Escherich (1857–1911). Many strains of *E. coli* are in mutualistic relationships with humans. However, some strains produce a potentially deadly toxin called Shiga toxin, which perforates cellular membranes in the large intestine, causing bloody diarrhea and peritonitis (inflammation of the inner linings of the abdominal cavity). Other *E. coli* strains may cause traveler's diarrhea, a less severe but very widespread disease. \nThe genus *Salmonella*, which belongs to the noncoliform group of *Enterobacteriaceae*, is interesting in that there is still no consensus about how many species it includes. Scientists have reclassified many of the groups they once thought to be species as **serotypes** (also called serovars), which are strains or variations of the same species of bacteria. Their classification is based on patterns of reactivity by animal antisera against molecules on the surface of the bacterial cells. A number of serotypes of *Salmonella* can cause salmonellosis, characterized by inflammation of the small and the large intestine, accompanied by fever, vomiting, and diarrhea. The species *S. enterobacterica* (serovar *typhi*) causes typhoid fever, with symptoms including fever, abdominal pain, and skin rashes (**[Figure 4.10](#page-172-0)**). \n \n**Figure 4.10** *Salmonella typhi* is the causative agent of typhoid fever. (credit: Centers for Disease Control and Prevention) \n**[Table 4.4](#page-172-1)** summarizes the characteristics of important genera of Gammaproteobacteria. \n#### **Example Genus Microscopic Morphology Unique Characteristics** *Beggiatoa* Gram-negative bacteria; disc-shaped or cylindrical Aquatic, live in water with high content of hydrogen disulfide; can cause problems for sewage treatment *Enterobacter* Gram-negative bacillus Facultative anaerobe; cause urinary and respiratory tract infections in hospitalized patients; implicated in the pathogenesis of obesity *Erwinia* Gram-negative bacillus Plant pathogen causing leaf spots and discoloration; may digest cellulose; prefer relatively low temperatures (25–30 °C) \n#### **Class Gammaproteobacteria** \n**Table 4.4** \n#### **Class Gammaproteobacteria** \n| Example
Genus | Microscopic
Morphology | Unique Characteristics |\n|------------------|----------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| Escherichia | Gram-negative
bacillus | Facultative anaerobe; inhabit the gastrointestinal tract of warm
blooded animals; some strains are mutualists, producing vitamin K;
others, like serotype E. coli O157:H7, are pathogens; E. coli has
been a model organism for many studies in genetics and molecular
biology |\n| Hemophilus | Gram-negative
bacillus | Pleomorphic, may appear as coccobacillus, aerobe, or facultative
anaerobe; grow on blood agar; pathogenic species can cause
respiratory infections, chancroid, and other diseases |\n| Klebsiella | Gram-negative
bacillus; appears
rounder and thicker
than other members
of Enterobacteriaceae | Facultative anaerobe, encapsulated, nonmotile; pathogenic species
may cause pneumonia, especially in people with alcoholism |\n| Legionella | Gram-negative
bacillus | Fastidious, grow on charcoal-buffered yeast extract; L. pneumophila
causes Legionnaires disease |\n| Methylomonas | Gram-negative
bacillus | Use methane as source of carbon and energy |\n| Proteus | Gram-negative
bacillus (pleomorphic) | Common inhabitants of the human gastrointestinal tract; motile;
produce urease; opportunistic pathogens; may cause urinary tract
infections and sepsis |\n| Pseudomonas | Gram-negative
bacillus | Aerobic; versatile; produce yellow and blue pigments, making them
appear green in culture; opportunistic, antibiotic-resistant pathogens
may cause wound infections, hospital-acquired infections, and
secondary infections in patients with cystic fibrosis |\n| Serratia | Gram-negative
bacillus | Motile; may produce red pigment; opportunistic pathogens
responsible for a large number of hospital-acquired infections |\n| Shigella | Gram-negative
bacillus | Nonmotile; dangerously pathogenic; produce Shiga toxin, which can
destroy cells of the gastrointestinal tract; can cause dysentery |\n| Vibrio | Gram-negative,
comma- or curved
rod-shaped bacteria | Inhabit seawater; flagellated, motile; may produce toxin that causes
hypersecretion of water and electrolytes in the gastrointestinal tract;
some species may cause serious wound infections |\n| Yersinia | Gram-negative
bacillus | Carried by rodents; human pathogens; Y. pestis causes bubonic
plague and pneumonic plague; Y. enterocolitica can be a pathogen
causing diarrhea in humans | \n**Table 4.4** \n \n• List two families of Gammaproteobacteria. \n#### **Deltaproteobacteria** \nThe **Deltaproteobacteria** is a small class of gram-negative Proteobacteria that includes sulfate-reducing bacteria \n(SRBs), so named because they use sulfate as the final electron acceptor in the electron transport chain. Few SRBs are pathogenic. However, the SRB *Desulfovibrio orale* is associated with periodontal disease (disease of the gums). \nDeltaproteobacteria also includes the genus *Bdellovibrio*, species of which are parasites of other gram-negative bacteria. *Bdellovibrio* invades the cells of the host bacterium, positioning itself in the periplasm, the space between the plasma membrane and the cell wall, feeding on the host's proteins and polysaccharides. The infection is lethal for the host cells. \nAnother type of Deltaproteobacteria, myxobacteria, lives in the soil, scavenging inorganic compounds. Motile and highly social, they interact with other bacteria within and outside their own group. They can form multicellular, macroscopic \"fruiting bodies\" (**[Figure 4.11](#page-174-0)**), structures that are still being studied by biologists and bacterial ecologists.[11] These bacteria can also form metabolically inactive myxospores. \n \n**Figure 4.11** Myxobacteria form fruiting bodies. (credit: modification of work by Michiel Vos) \n**[Table 4.5](#page-174-1)** summarizes the characteristics of several important genera of Deltaproteobacteria. \n#### **Class Deltaproteobacteria** \n| Genus | Microscopic Morphology | Unique characteristics |\n|----------------------------------------------|-----------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------|\n| Bdellovibrio | Gram-negative, comma
shaped rod | Obligate aerobes; motile; parasitic (infecting other
bacteria) |\n| Desulfovibrio
(formerly
Desufuromonas) | Gram-negative, comma
shaped rod | Reduce sulfur; can be used for removal of toxic and
radioactive waste |\n| Myxobacterium | Gram-negative, coccoid
bacteria forming colonies
(swarms) | Live in soil; can move by gliding; used as a model
organism for studies of intercellular communication
(signaling) | \n**Table 4.5** \n11. H. Reichenbach. \"Myxobacteria, Producers of Novel Bioactive Substances.\" *Journal of Industrial Microbiology & Biotechnology* 27 no. 3 (2001):149–156. \n \n• What type of Deltaproteobacteria forms fruiting bodies?\n\nThe smallest class of Proteobacteria is **Epsilonproteobacteria**, which are gram-negative microaerophilic bacteria (meaning they only require small amounts of oxygen in their environment). Two clinically relevant genera of Epsilonproteobacteria are *Campylobacter* and *Helicobacter*, both of which include human pathogens. *Campylobacter* can cause food poisoning that manifests as severe enteritis (inflammation in the small intestine). This condition, caused by the species *C. jejuni*, is rather common in developed countries, usually because of eating contaminated poultry products. Chickens often harbor *C. jejuni* in their gastrointestinal tract and feces, and their meat can become contaminated during processing. \nWithin the genus *Helicobacter,* the helical, flagellated bacterium *H. pylori* has been identified as a beneficial member of the stomach microbiota, but it is also the most common cause of chronic gastritis and ulcers of the stomach and duodenum (**[Figure 4.12](#page-175-0)**). Studies have also shown that *H. pylori* is linked to stomach cancer.[12] *H. pylori* is somewhat unusual in its ability to survive in the highly acidic environment of the stomach. It produces urease and other enzymes that modify its environment to make it less acidic. \n \n**Figure 4.12** *Helicobacter pylori* can cause chronic gastritis, which can lead to ulcers and stomach cancer. \n**[Table 4.6](#page-175-1)** summarizes the characteristics of the most clinically relevant genera of Epsilonproteobacteria. \n#### **Class Epsilonproteobacteria** \n| Example
Genus | Microscopic
Morphology | Unique Characteristics |\n|------------------|----------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------|\n| Campylobacter | Gram-negative,
spiral-shaped
rod | Aerobic (microaerophilic); often infects chickens; may infect humans via
undercooked meat, causing severe enteritis |\n| Helicobacter | Gram-negative,
spiral-shaped
rod | Aerobic (microaerophilic) bacterium; can damage the inner lining of the
stomach, causing chronic gastritis, peptic ulcers, and stomach cancer | \n#### **Table 4.6** \n12. S. Suerbaum, P. Michetti. \"*Helicobacter pylori* infection.\" *New England Journal of Medicine* 347 no. 15 (2002):1175–1186. \nChapter 4 | Prokaryotic Diversity 167 \n \n• Name two Epsilonproteobacteria that cause gastrointestinal disorders.",
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"page_content": "#### **Learning Objectives** \n- Describe the unique features of nonproteobacteria gram-negative bacteria\n- Give an example of a nonproteobacteria bacterium in each category\n- Describe the unique features of phototrophic bacteria\n- Identify phototrophic bacteria \nThe majority of the gram-negative bacteria belong to the phylum Proteobacteria, discussed in the previous section. Those that do not are called the nonproteobacteria. In this section, we will describe three classes of gram-negative nonproteobacteria: the spirochetes, the CFB group, and the Planctomycetes. A diverse group of phototrophic bacteria that includes Proteobacteria and nonproteobacteria will be discussed at the end of this section.\n\nSpirochetes are characterized by their long (up to 250 μm), spiral-shaped bodies. Most **spirochetes** are also very thin, which makes it difficult to examine gram-stained preparations under a conventional brightfield microscope. Darkfield fluorescent microscopy is typically used instead. Spirochetes are also difficult or even impossible to culture. They are highly motile, using their axial filament to propel themselves. The axial filament is similar to a flagellum, but it wraps around the cell and runs inside the cell body of a spirochete in the periplasmic space between the outer membrane and the plasma membrane (**[Figure 4.13](#page-177-0)**). \n \n**Figure 4.13** Spirochetes are typically observed using darkfield microscopy (left). However, electron microscopy (top center, bottom center) provides a more detailed view of their cellular morphology. The flagella found between the inner and outer membranes of spirochetes wrap around the bacterium, causing a twisting motion used for locomotion. (credit \"spirochetes\" micrograph: modification of work by Centers for Disease Control and Prevention; credit \"SEM/ TEM\": modification of work by Guyard C, Raffel SJ, Schrumpf ME, Dahlstrom E, Sturdevant D, Ricklefs SM, Martens C, Hayes SF, Fischer ER, Hansen BT, Porcella SF, Schwan TG) \nSeveral genera of spirochetes include human pathogens. For example, the genus *Treponema* includes a species *T. pallidum*, which is further classified into four subspecies: *T. pallidum pallidum*, *T. pallidum pertenue, T. pallidum carateum,* and *T. pallidum endemicum*. The subspecies *T. pallidum pallidum* causes the sexually transmitted infection known as syphilis, the third most prevalent sexually transmitted bacterial infection in the United States, after chlamydia and gonorrhea. The other subspecies of *T. pallidum* cause tropical infectious diseases of the skin, bones, and joints. \nAnother genus of spirochete, *Borrelia*, contains a number of pathogenic species. *B. burgdorferi* causes Lyme disease, which is transmitted by several genera of ticks (notably *Ixodes* and *Amblyomma*) and often produces a \"bull's eye\" rash, fever, fatigue, and, sometimes, debilitating arthritis. *B. recurrens* causes a condition known as relapsing fever. **[Appendix D](#page-1248-0)** lists the genera, species, and related diseases for spirochetes. \n \n• Why do scientists typically use darkfield fluorescent microscopy to visualize spirochetes?\n\nThe gram-negative nonproteobacteria of the genera *Cytophaga*, *Fusobacterium*, and *Bacteroides* are classified together as a phylum and called the **CFB group**. Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA. They are rod-shaped bacteria adapted to anaerobic environments, such as the tissue of the gums, gut, and rumen of ruminating animals. CFB bacteria are avid fermenters, able to process cellulose in rumen, thus enabling ruminant animals to obtain carbon and energy from grazing. \n*Cytophaga* are motile aquatic bacteria that glide. *Fusobacteria* inhabit the human mouth and may cause severe infectious diseases. The largest genus of the CFB group is *Bacteroides*, which includes dozens of species that are prevalent inhabitants of the human large intestine, making up about 30% of the entire gut microbiome (**[Figure 4.14](#page-178-0)**). One gram of human feces contains up to 100 billion *Bacteroides* cells. Most *Bacteroides* are mutualistic. They benefit from nutrients they find in the gut, and humans benefit from their ability to prevent pathogens from colonizing the large intestine. Indeed, when populations of *Bacteroides* are reduced in the gut—as often occurs when a patient takes antibiotics—the gut becomes a more favorable environment for pathogenic bacteria and fungi, which can cause secondary infections. \n \n**Figure 4.14** *Bacteroides* comprise up to 30% of the normal microbiota in the human gut. (credit: NOAA) \nOnly a few species of *Bacteroides* are pathogenic. *B. melaninogenicus*, for example, can cause wound infections in patients with weakened immune systems. \n \n• Why are *Cytophaga*, *Fusobacterium*, and *Bacteroides* classified together as the CFB group?\n\nThe Planctomycetes are found in aquatic environments, inhabiting freshwater, saltwater, and brackish water. Planctomycetes are unusual in that they reproduce by budding, meaning that instead of one maternal cell splitting into two equal daughter cells in the process of binary fission, the mother cell forms a bud that detaches from the mother cell and lives as an independent cell. These so-called swarmer cells are motile and not attached to a surface. However, they will soon differentiate into sessile (immobile) cells with an appendage called a holdfast that allows them to attach to surfaces in the water (**[Figure 4.15](#page-179-0)**). Only the sessile cells are able to reproduce. \n \n \n**Figure 4.15** (a) Sessile Planctomycetes have a holdfast that allows them to adhere to surfaces in aquatic environments. (b) Swarmers are motile and lack a holdfast. (credit: modification of work by American Society for Microbiology) \n**[Table 4.7](#page-179-1)** summarizes the characteristics of some of the most clinically relevant genera of nonproteobacteria. \n#### **Nonproteobacteria** \n| Example Genus | Microscopic Morphology | Unique Characteristics | |\n|------------------|-----------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--|\n| Bacteroides | Gram-negative bacillus | Obligate anaerobic bacteria; abundant in the human
gastrointestinal tract; usually mutualistic, although
some species are opportunistic pathogens | |\n| Cytophaga | Gram-negative bacillus | Motile by gliding; live in soil or water; decompose
cellulose; may cause disease in fish | |\n| Fusobacterium | Gram-negative bacillus with
pointed ends | Anaerobic; form; biofilms; some species cause
disease in humans (periodontitis, ulcers) | |\n| Leptospira | Spiral-shaped bacterium
(spirochetes); gram negative-like
(better viewed by darkfield
microscopy); very thin | Aerobic, abundant in shallow water reservoirs; infect
rodents and domestic animals; can be transmitted to
humans by infected animals' urine; may cause severe
disease | |\n| Sphingobacterium | Gram-negative bacillus | Oxidase positive; nonmotile; contain high amounts of
sphingophospholipids; rarely cause disease in
humans | |\n| Treponema | Gram-negative-like spirochete;
very thin; better viewed by
darkfield microscopy | Motile; do not grow in culture; T. pallidum (subspecies
T. pallidum pallidum) causes syphilis | | \n**Table 4.7** \n \n• How do Planctomycetes reproduce?\n\nThe **phototrophic bacteria** are a large and diverse category of bacteria that do not represent a taxon but, rather, a group of bacteria that use sunlight as their primary source of energy. This group contains both Proteobacteria and nonproteobacteria. They use solar energy to synthesize ATP through photosynthesis. When they produce oxygen, they perform oxygenic photosynthesis. When they do not produce oxygen, they perform anoxygenic photosynthesis. With the exception of some cyanobacteria, the majority of phototrophic bacteria perform anoxygenic photosynthesis. \nOne large group of phototrophic bacteria includes the purple or green bacteria that perform photosynthesis with the help of **bacteriochlorophylls**, which are green, purple, or blue pigments similar to chlorophyll in plants. Some of these bacteria have a varying amount of red or orange pigments called carotenoids. Their color varies from orange to red to purple to green (**[Figure 4.16](#page-180-0)**), and they are able to absorb light of various wavelengths. Traditionally, these bacteria are classified into sulfur and nonsulfur bacteria; they are further differentiated by color. \n \n**Figure 4.16** Purple and green sulfur bacteria use bacteriochlorophylls to perform photosynthesis. \nThe sulfur bacteria perform anoxygenic photosynthesis, using sulfites as electron donors and releasing free elemental sulfur. Nonsulfur bacteria use organic substrates, such as succinate and malate, as donors of electrons. \nThe **purple sulfur bacteria** oxidize hydrogen sulfide into elemental sulfur and sulfuric acid and get their purple color from the pigments bacteriochlorophylls and carotenoids. Bacteria of the genus *Chromatium* are purple sulfur Gammaproteobacteria. These microorganisms are strict anaerobes and live in water. They use carbon dioxide as their only source of carbon, but their survival and growth are possible only in the presence of sulfites, which they use as electron donors. *Chromatium* has been used as a model for studies of bacterial photosynthesis since the 1950s.[13] \nThe **green sulfur bacteria** use sulfide for oxidation and produce large amounts of green bacteriochlorophyll. The genus *Chlorobium* is a green sulfur bacterium that is implicated in climate change because it produces methane, a greenhouse gas. These bacteria use at least four types of chlorophyll for photosynthesis. The most prevalent of these, bacteriochlorophyll, is stored in special vesicle-like organelles called chlorosomes. \nPurple nonsulfur bacteria are similar to purple sulfur bacteria, except that they use hydrogen rather than hydrogen sulfide for oxidation. Among the **purple nonsulfur bacteria** is the genus *Rhodospirillum*. These microorganisms are facultative anaerobes, which are actually pink rather than purple, and can metabolize (\"fix\") nitrogen. They may be valuable in the field of biotechnology because of their potential ability to produce biological plastic and hydrogen fuel.[14] \nThe **green nonsulfur bacteria** are similar to green sulfur bacteria but they use substrates other than sulfides for oxidation. *Chloroflexus* is an example of a green nonsulfur bacterium. It often has an orange color when it grows in the dark, but it becomes green when it grows in sunlight. It stores bacteriochlorophyll in chlorosomes, similar to *Chlorobium*, and performs anoxygenic photosynthesis, using organic sulfites (low concentrations) or molecular hydrogen as electron donors, so it can survive in the dark if oxygen is available. *Chloroflexus* does not have flagella but can glide, like *Cytophaga*. It grows at a wide range of temperatures, from 35 °C to 70 °C, thus can be thermophilic. \n13. R.C. Fuller et al. \"Carbon Metabolism in *Chromatium*.\" *Journal of Biological Chemistry* 236 (1961):2140–2149. \n14. T.T. Selao et al. \"Comparative Proteomic Studies in *Rhodospirillum rubrum* Grown Under Different Nitrogen Conditions.\" *Journal of Proteome Research* 7 no. 8 (2008):3267–3275. \nAnother large, diverse group of phototrophic bacteria compose the phylum **Cyanobacteria**; they get their bluegreen color from the chlorophyll contained in their cells (**[Figure 4.17](#page-181-0)**). Species of this group perform oxygenic photosynthesis, producing megatons of gaseous oxygen. Scientists hypothesize that cyanobacteria played a critical role in the change of our planet's anoxic atmosphere 1–2 billion years ago to the oxygen-rich environment we have today.[15] \n \n \n**Figure 4.17** (a) *Microcystis aeruginosa* is a type of cyanobacteria commonly found in freshwater environments. (b) In warm temperatures, *M. aeruginosa* and other cyanobacteria can multiply rapidly and produce neurotoxins, resulting in blooms that are harmful to fish and other aquatic animals. (credit a: modification of work by Dr. Barry H. Rosen/U.S. Geological Survey; credit b: modification of work by NOAA) \nCyanobacteria have other remarkable properties. Amazingly adaptable, they thrive in many habitats, including marine and freshwater environments, soil, and even rocks. They can live at a wide range of temperatures, even in the extreme temperatures of the Antarctic. They can live as unicellular organisms or in colonies, and they can be filamentous, forming sheaths or biofilms. Many of them fix nitrogen, converting molecular nitrogen into nitrites and nitrates that other bacteria, plants, and animals can use. The reactions of nitrogen fixation occur in specialized cells called heterocysts. \nPhotosynthesis in Cyanobacteria is oxygenic, using the same type of chlorophyll a found in plants and algae as the primary photosynthetic pigment. Cyanobacteria also use phycocyanin and cyanophycin, two secondary photosynthetic pigments that give them their characteristic blue color. They are located in special organelles called phycobilisomes and in folds of the cellular membrane called thylakoids, which are remarkably similar to the photosynthetic apparatus of plants. Scientists hypothesize that plants originated from endosymbiosis of ancestral eukaryotic cells and ancestral photosynthetic bacteria.[16] Cyanobacteria are also an interesting object of research in biochemistry,[17] with studies investigating their potential as biosorbents[18] and products of human nutrition.[19] \nUnfortunately, cyanobacteria can sometimes have a negative impact on human health. Genera such as *Microcystis* can form harmful cyanobacterial blooms, forming dense mats on bodies of water and producing large quantities of toxins that can harm wildlife and humans. These toxins have been implicated in tumors of the liver and diseases of the nervous system in animals and humans.[20] \n15. A. De los Rios et al. \"Ultrastructural and Genetic Characteristics of Endolithic Cyanobacterial Biofilms Colonizing Antarctic Granite Rocks.\" *FEMS Microbiology Ecology* 59 no. 2 (2007):386–395. \n16. T. Cavalier-Smith. \"Membrane Heredity and Early Chloroplast Evolution.\" *Trends in Plant Science* 5 no. 4 (2000):174–182. \n17. S. Zhang, D.A. Bryant. \"The Tricarboxylic Acid Cycle in Cyanobacteria.\" *Science* 334 no. 6062 (2011):1551–1553. \n18. A. Cain et al. \"Cyanobacteria as a Biosorbent for Mercuric Ion.\" Bioresource Technology 99 no. 14 (2008):6578–6586. \n19. C.S. Ku et al. \"Edible Blue-Green Algae Reduce the Production of Pro-Inflammatory Cytokines by Inhibiting NF-κB Pathway in Macrophages and Splenocytes.\" *Biochimica et Biophysica Acta* 1830 no. 4 (2013):2981–2988. \n20. I. Stewart et al. Cyanobacterial Poisoning in Livestock, Wild Mammals and Birds – an Overview. *Advances in Experimental Medicine and Biology* 619 (2008):613–637. \nChapter 4 | Prokaryotic Diversity 173 \n**Table 4.8** summarizes the characteristics of important phototrophic bacteria. \n#### **Phototrophic Bacteria** \n| Phylum | Class | Example
Genus or
Species | Common
Name | Oxygenic or
Anoxygenic | Sulfur
Deposition |\n|---------------------------|---------------------|--------------------------------|---------------------------------|---------------------------|----------------------|\n| Cyanobacteria | Cyanophyceae | Microcystis
aeruginosa | Blue-green
bacteria | Oxygenic | None |\n| Chlorobi | Chlorobia | Chlorobium | Green sulfur
bacteria | Anoxygenic | Outside the cell |\n| Chloroflexi
(Division) | Chloroflexi | Chloroflexus | Green
nonsulfur
bacteria | Anoxygenic | None |\n| | Alphaproteobacteria | Rhodospirillum | Purple
nonsulfur
bacteria | Anoxygenic | None |\n| Proteobacteria | Betaproteobacteria | Rhodocyclus | Purple
nonsulfur
bacteria | Anoxygenic | None |\n| | Gammaproteobacteria | Chromatium | Purple sulfur
bacteria | Anoxygenic | Inside the cell | \n**Table 4.8** \n \n· What characteristic makes phototrophic bacteria different from other prokaryotes?",
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"page_content": "#### **Learning Objectives** \n- Describe the unique features of each category of high G+C and low G+C gram-positive bacteria\n- Identify similarities and differences between high G+C and low G+C bacterial groups\n- Give an example of a bacterium of high G+C and low G+C group commonly associated with each category \nProkaryotes are identified as gram-positive if they have a multiple layer matrix of peptidoglycan forming the cell wall. Crystal violet, the primary stain of the Gram stain procedure, is readily retained and stabilized within this matrix, causing gram-positive prokaryotes to appear purple under a brightfield microscope after Gram staining. For many years, the retention of Gram stain was one of the main criteria used to classify prokaryotes, even though some prokaryotes did not readily stain with either the primary or secondary stains used in the Gram stain procedure. \nAdvances in nucleic acid biochemistry have revealed additional characteristics that can be used to classify grampositive prokaryotes, namely the guanine to cytosine ratios (G+C) in DNA and the composition of 16S rRNA subunits. Microbiologists currently recognize two distinct groups of gram-positive, or weakly staining gram-positive, prokaryotes. The class Actinobacteria comprises the **high G+C gram-positive bacteria**, which have more than 50% guanine and cytosine nucleotides in their DNA. The class Bacilli comprises **low G+C gram-positive bacteria**, which have less than 50% of guanine and cytosine nucleotides in their DNA. \n174 Chapter 4 | Prokaryotic Diversity\n\nThe name Actinobacteria comes from the Greek words for *rays* and *small rod*, but Actinobacteria are very diverse. Their microscopic appearance can range from thin filamentous branching rods to coccobacilli. Some Actinobacteria are very large and complex, whereas others are among the smallest independently living organisms. Most Actinobacteria live in the soil, but some are aquatic. The vast majority are aerobic. One distinctive feature of this group is the presence of several different peptidoglycans in the cell wall. \nThe genus *Actinomyces* is a much studied representative of Actinobacteria. *Actinomyces* spp. play an important role in soil ecology, and some species are human pathogens. A number of *Actinomyces* spp. inhabit the human mouth and are opportunistic pathogens, causing infectious diseases like periodontitis (inflammation of the gums) and oral abscesses. The species *A. israelii* is an anaerobe notorious for causing endocarditis (inflammation of the inner lining of the heart) (**[Figure 4.18](#page-183-0)**). \n \n \n \n**Figure 4.18** (a) *Actinomyces israelii* (false-color scanning electron micrograph [SEM]) has a branched structure. (b) *Corynebacterium diphtheria* causes the deadly disease diphtheria. Note the distinctive palisades. (c) The gramvariable bacterium *Gardnerella vaginalis* causes bacterial vaginosis in women. This micrograph shows a Pap smear from a woman with vaginosis. (credit a: modification of work by \"GrahamColm\"/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by Mwakigonja AR, Torres LM, Mwakyoma HA, Kaaya EE) \nThe genus *Mycobacterium* is represented by bacilli covered with a mycolic acid coat. This waxy coat protects the bacteria from some antibiotics, prevents them from drying out, and blocks penetration by Gram stain reagents (see **[Staining Microscopic Specimens](#page-80-0)**). Because of this, a special acid-fast staining procedure is used to visualize these bacteria. The genus *Mycobacterium* is an important cause of a diverse group of infectious diseases. *M. tuberculosis* is the causative agent of tuberculosis, a disease that primarily impacts the lungs but can infect other parts of the body as well. It has been estimated that one-third of the world's population has been infected with *M. tuberculosis* and millions of new infections occur each year. Treatment of *M. tuberculosis* is challenging and requires patients to take a combination of drugs for an extended time. Complicating treatment even further is the development and spread of multidrug-resistant strains of this pathogen. \nAnother pathogenic species, *M. leprae*, is the cause of Hansen's disease (leprosy), a chronic disease that impacts peripheral nerves and the integrity of the skin and mucosal surface of the respiratory tract. Loss of pain sensation and the presence of skin lesions increase susceptibility to secondary injuries and infections with other pathogens. \nBacteria in the genus *Corynebacterium* contain diaminopimelic acid in their cell walls, and microscopically often form *palisades*, or pairs of rod-shaped cells resembling the letter V. Cells may contain metachromatic granules, intracellular storage of inorganic phosphates that are useful for identification of *Corynebacterium*. The vast majority of *Corynebacterium* spp. are nonpathogenic; however, *C. diphtheria* is the causative agent of diphtheria, a disease that can be fatal, especially in children (**[Figure 4.18](#page-183-0)**). *C. diphtheria* produces a toxin that forms a pseudomembrane in the patient's throat, causing swelling, difficulty breathing, and other symptoms that can become serious if untreated. \nThe genus *Bifidobacterium* consists of filamentous anaerobes, many of which are commonly found in the gastrointestinal tract, vagina, and mouth. In fact, *Bifidobacterium* spp. constitute a substantial part of the human gut microbiota and are frequently used as probiotics and in yogurt production. \nThe genus *Gardnerella*, contains only one species, *G. vaginalis*. This species is defined as \"gram-variable\" because its small coccobacilli do not show consistent results when Gram stained (**[Figure 4.18](#page-183-0)**). Based on its genome, it is placed into the high G+C gram-positive group. *G. vaginalis* can cause bacterial vaginosis in women; symptoms are typically mild or even undetectable, but can lead to complications during pregnancy. \n**[Table 4.9](#page-184-0)** summarizes the characteristics of some important genera of Actinobacteria. Additional information on Actinobacteria appears in **[Appendix D](#page-1244-1)**. \n#### **Actinobacteria: High G+C Gram-Positive** \n| Example Genus | Microscopic
Morphology | Unique Characteristics |\n|-------------------|---------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| Actinomyces | Gram-positive
bacillus; in colonies,
shows fungus-like
threads (hyphae) | Facultative anaerobes; in soil, decompose organic matter; in the
human mouth, may cause gum disease |\n| Arthrobacter | Gram-positive
bacillus (at the
exponential stage of
growth) or coccus (in
stationary phase) | Obligate aerobes; divide by \"snapping,\" forming V-like pairs of
daughter cells; degrade phenol, can be used in bioremediation |\n| Bifidobacterium | Gram-positive,
filamentous
actinobacterium | Anaerobes commonly found in human gut microbiota |\n| Corynebacterium | Gram-positive
bacillus | Aerobes or facultative anaerobes; form palisades; grow slowly;
require enriched media in culture; C. diphtheriae causes
diphtheria |\n| Frankia | Gram-positive,
fungus-like
(filamentous) bacillus | Nitrogen-fixing bacteria; live in symbiosis with legumes |\n| Gardnerella | Gram-variable
coccobacillus | Colonize the human vagina, may alter the microbial ecology, thus
leading to vaginosis |\n| Micrococcus | Gram-positive
coccus, form
microscopic clusters | Ubiquitous in the environment and on the human skin; oxidase
positive (as opposed to morphologically similar S. aureus); some
are opportunistic pathogens |\n| Mycobacterium | Gram-positive, acid
fast bacillus | Slow growing, aerobic, resistant to drying and phagocytosis;
covered with a waxy coat made of mycolic acid; M. tuberculosis
causes tuberculosis; M. leprae causes leprosy |\n| Nocardia | Weakly gram-positive
bacillus; forms acid
fast branches | May colonize the human gingiva; may cause severe pneumonia
and inflammation of the skin |\n| Propionibacterium | Gram-positive
bacillus | Aerotolerant anaerobe; slow-growing; P. acnes reproduces in the
human sebaceous glands and may cause or contribute to acne |\n| Rhodococcus | Gram-positive
bacillus | Strict aerobe; used in industry for biodegradation of pollutants; R.
fascians is a plant pathogen, and R. equi causes pneumonia in
foals | \n**Table 4.9** \n#### **Actinobacteria: High G+C Gram-Positive** \n| Example Genus | Microscopic
Morphology | Unique Characteristics |\n|---------------|---------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| Streptomyces | Gram-positive,
fungus-like
(filamentous) bacillus | Very diverse genus (>500 species); aerobic, spore-forming
bacteria; scavengers, decomposers found in soil (give the soil its
\"earthy\" odor); used in pharmaceutical industry as antibiotic
producers (more than two-thirds of clinically useful antibiotics) | \n**Table 4.9** \n \n• What is one distinctive feature of Actinobacteria? \n#### **Low G+C Gram-positive Bacteria** \nThe low G+C gram-positive bacteria have less than 50% guanine and cytosine in their DNA, and this group of bacteria includes a number of genera of bacteria that are pathogenic. \n#### **Clinical Focus** \n#### **Part 3** \nBased on her symptoms, Marsha's doctor suspected that she had a case of tuberculosis. Although less common in the United States, tuberculosis is still extremely common in many parts of the world, including Nigeria. Marsha's work there in a medical lab likely exposed her to *Mycobacterium tuberculosis*, the bacterium that causes tuberculosis. \nMarsha's doctor ordered her to stay at home, wear a respiratory mask, and confine herself to one room as much as possible. He also said that Marsha had to take one semester off school. He prescribed isoniazid and rifampin, antibiotics used in a drug cocktail to treat tuberculosis, which Marsha was to take three times a day for at least three months. \n• Why did the doctor order Marsha to stay home for three months? \n*Jump to the [next](#page-190-0) Clinical Focus box. Go back to the [previous](#page-170-0) Clinical Focus box.* \n#### **Clostridia** \nOne large and diverse class of low G+C gram-positive bacteria is Clostridia. The best studied genus of this class is *Clostridium*. These rod-shaped bacteria are generally obligate anaerobes that produce endospores and can be found in anaerobic habitats like soil and aquatic sediments rich in organic nutrients. The endospores may survive for many years. \n*Clostridium* spp. produce more kinds of protein toxins than any other bacterial genus, and several species are human pathogens. *C. perfringens* is the third most common cause of food poisoning in the United States and is the causative agent of an even more serious disease called gas gangrene. Gas gangrene occurs when *C. perfringens* endospores enter a wound and germinate, becoming viable bacterial cells and producing a toxin that can cause the necrosis (death) of tissue. *C. tetani*, which causes tetanus, produces a neurotoxin that is able to enter neurons, travel to regions of the central nervous system where it blocks the inhibition of nerve impulses involved in muscle contractions, and cause a life-threatening spastic paralysis. *C. botulinum* produces botulinum neurotoxin, the most lethal biological toxin known. Botulinum toxin is responsible for rare but frequently fatal cases of botulism. The toxin blocks the release of acetylcholine in neuromuscular junctions, causing flaccid paralysis. In very small concentrations, botulinum toxin has been used to treat muscle pathologies in humans and in a cosmetic procedure to eliminate wrinkles. *C. difficile* is a common source of hospital-acquired infections (**[Figure 4.19](#page-186-0)**) that can result in serious and even fatal cases of colitis (inflammation of the large intestine). Infections often occur in patients who are immunosuppressed or undergoing antibiotic therapy that alters the normal microbiota of the gastrointestinal tract. **[Appendix D](#page-1245-0)** lists the genera, species, and related diseases for Clostridia. \n \n**Figure 4.19** *Clostridium difficile*, a gram-positive, rod-shaped bacterium, causes severe colitis and diarrhea, often after the normal gut microbiota is eradicated by antibiotics. (credit: modification of work by Centers for Disease Control and Prevention) \n#### **Lactobacillales** \nThe order Lactobacillales comprises low G+C gram-positive bacteria that include both bacilli and cocci in the genera *Lactobacillus*, *Leuconostoc*, *Enterococcus*, and *Streptococcus*. Bacteria of the latter three genera typically are spherical or ovoid and often form chains. \n*Streptococcus*, the name of which comes from the Greek word for *twisted chain*, is responsible for many types of infectious diseases in humans. Species from this genus, often referred to as streptococci, are usually classified by serotypes called Lancefield groups, and by their ability to lyse red blood cells when grown on blood agar. \n*S. pyogenes* belongs to the Lancefield group A, β-hemolytic *Streptococcus*. This species is considered a pyogenic pathogen because of the associated pus production observed with infections it causes (**[Figure 4.20](#page-187-0)**). *S. pyogenes* is the most common cause of bacterial pharyngitis (strep throat); it is also an important cause of various skin infections that can be relatively mild (e.g., impetigo) or life threatening (e.g., necrotizing fasciitis, also known as flesh eating disease), life threatening. \n \n \n**Figure 4.20** (a) A gram-stained specimen of *Streptococcus pyogenes* shows the chains of cocci characteristic of this organism's morphology. (b) *S. pyogenes* on blood agar shows characteristic lysis of red blood cells, indicated by the halo of clearing around colonies. (credit a, b: modification of work by American Society for Microbiology) \nThe nonpyogenic (i.e., not associated with pus production) streptococci are a group of streptococcal species that are not a taxon but are grouped together because they inhabit the human mouth. The nonpyogenic streptococci do not belong to any of the Lancefield groups. Most are commensals, but a few, such as *S. mutans*, are implicated in the development of dental caries. \n*S. pneumoniae* (commonly referred to as pneumococcus), is a *Streptococcus* species that also does not belong to any Lancefield group. *S. pneumoniae* cells appear microscopically as diplococci, pairs of cells, rather than the long chains typical of most streptococci. Scientists have known since the 19th century that *S. pneumoniae* causes pneumonia and other respiratory infections. However, this bacterium can also cause a wide range of other diseases, including meningitis, septicemia, osteomyelitis, and endocarditis, especially in newborns, the elderly, and patients with immunodeficiency. \n#### **Bacilli** \nThe name of the class Bacilli suggests that it is made up of bacteria that are bacillus in shape, but it is a morphologically diverse class that includes bacillus-shaped and cocccus-shaped genera. Among the many genera in this class are two that are very important clinically: *Bacillus* and *Staphylococcus*. \nBacteria in the genus *Bacillus* are bacillus in shape and can produce endospores. They include aerobes or facultative anaerobes. A number of *Bacillus* spp. are used in various industries, including the production of antibiotics (e.g., barnase), enzymes (e.g., alpha-amylase, BamH1 restriction endonuclease), and detergents (e.g., subtilisin). \nTwo notable pathogens belong to the genus *Bacillus. B. anthracis* is the pathogen that causes anthrax, a severe disease that affects wild and domesticated animals and can spread from infected animals to humans. Anthrax manifests in humans as charcoal-black ulcers on the skin, severe enterocolitis, pneumonia, and brain damage due to swelling. If untreated, anthrax is lethal. *B. cereus*, a closely related species, is a pathogen that may cause food poisoning. It is a rod-shaped species that forms chains. Colonies appear milky white with irregular shapes when cultured on blood agar (**[Figure 4.21](#page-188-0)**). One other important species is *B. thuringiensis*. This bacterium produces a number of substances used as insecticides because they are toxic for insects. \nChapter 4 | Prokaryotic Diversity 179 \n \n**Figure 4.21** (a) In this gram-stained specimen, the violet rod-shaped cells forming chains are the gram-positive bacteria *Bacillus cereus*. The small, pink cells are the gram-negative bacteria *Escherichia coli*. (b) In this culture, white colonies of *B. cereus* have been grown on sheep blood agar. (credit a: modification of work by \"Bibliomaniac 15\"/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention) \nThe genus *Staphylococcus* also belongs to the class Bacilli, even though its shape is coccus rather than a bacillus. The name *Staphylococcus* comes from a Greek word for *bunches of grapes*, which describes their microscopic appearance in culture (**[Figure 4.22](#page-188-1)**). *Staphylococcus* spp. are facultative anaerobic, halophilic, and nonmotile. The two beststudied species of this genus are *S. epidermidis* and *S. aureus*. \n \n**Figure 4.22** This SEM of *Staphylococcus aureus* illustrates the typical \"grape-like\" clustering of cells. (credit: modification of work by Centers for Disease Control and Prevention) \n*S. epidermidis*, whose main habitat is the human skin, is thought to be nonpathogenic for humans with healthy immune systems, but in patients with immunodeficiency, it may cause infections in skin wounds and prostheses (e.g., artificial joints, heart valves)*. S. epidermidis* is also an important cause of infections associated with intravenous catheters. This makes it a dangerous pathogen in hospital settings, where many patients may be immunocompromised. \nStrains of *S. aureus* cause a wide variety of infections in humans, including skin infections that produce boils, carbuncles, cellulitis, or impetigo. Certain strains of *S. aureus* produce a substance called enterotoxin, which can cause severe enteritis, often called staph food poisoning. Some strains of *S. aureus* produce the toxin responsible for toxic shock syndrome, which can result in cardiovascular collapse and death. \nMany strains of *S. aureus* have developed resistance to antibiotics. Some antibiotic-resistant strains are designated as methicillin-resistant *S. aureus* (MRSA) and vancomycin-resistant *S. aureus* (VRSA). These strains are some of the most difficult to treat because they exhibit resistance to nearly all available antibiotics, not just methicillin and vancomycin. Because they are difficult to treat with antibiotics, infections can be lethal. MRSA and VRSA are also contagious, posing a serious threat in hospitals, nursing homes, dialysis facilities, and other places where there are large populations of elderly, bedridden, and/or immunocompromised patients. **[Appendix D](#page-1245-0)** lists the genera, species, and related diseases for bacilli. \n#### **Mycoplasmas** \nAlthough *Mycoplasma* spp. do not possess a cell wall and, therefore, are not stained by Gram-stain reagents, this genus is still included with the low G+C gram-positive bacteria. The genus *Mycoplasma* includes more than 100 species, which share several unique characteristics. They are very small cells, some with a diameter of about 0.2 μm, which is smaller than some large viruses. They have no cell walls and, therefore, are **pleomorphic**, meaning that they may take on a variety of shapes and can even resemble very small animal cells. Because they lack a characteristic shape, they can be difficult to identify. One species, *M. pneumoniae*, causes the mild form of pneumonia known as \"walking pneumonia\" or \"atypical pneumonia.\" This form of pneumonia is typically less severe than forms caused by other bacteria or viruses. \n**[Table 4.10](#page-189-0)** summarizes the characteristics of notable genera low G+C Gram-positive bacteria. \n#### **Bacilli: Low G+C Gram-Positive Bacteria** \n| Example
Genus | Microscopic Morphology | Unique Characteristics |\n|------------------|---------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| Bacillus | Large, gram-positive bacillus | Aerobes or facultative anaerobes; form endospores; B.
anthracis causes anthrax in cattle and humans, B. cereus
may cause food poisoning |\n| Clostridium | Gram-positive bacillus | Strict anaerobes; form endospores; all known species are
pathogenic, causing tetanus, gas gangrene, botulism, and
colitis |\n| Enterococcus | Gram-positive coccus; forms
microscopic pairs in culture
(resembling Streptococcus
pneumoniae) | Anaerobic aerotolerant bacteria, abundant in the human
gut, may cause urinary tract and other infections in the
nosocomial environment |\n| Lactobacillus | Gram-positive bacillus | Facultative anaerobes; ferment sugars into lactic acid; part
of the vaginal microbiota; used as probiotics |\n| Leuconostoc | Gram-positive coccus; may
form microscopic chains in
culture | Fermenter, used in food industry to produce sauerkraut and
kefir |\n| Mycoplasma | The smallest bacteria;
appear pleomorphic under
electron microscope | Have no cell wall; classified as low G+C Gram-positive
bacteria because of their genome; M. pneumoniae causes
\"walking\" pneumonia |\n| Staphylococcus | Gram-positive coccus; forms
microscopic clusters in
culture that resemble
bunches of grapes | Tolerate high salt concentration; facultative anaerobes;
produce catalase; S. aureus can also produce coagulase
and toxins responsible for local (skin) and generalized
infections |\n| Streptococcus | Gram-positive coccus; forms
chains or pairs in culture | Diverse genus; classified into groups based on sharing
certain antigens; some species cause hemolysis and may
produce toxins responsible for human local (throat) and
generalized disease | \n**Table 4.10** \n#### **Bacilli: Low G+C Gram-Positive Bacteria** \n| Example
Genus | Microscopic Morphology | Unique Characteristics |\n|------------------|------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|\n| Ureaplasma | Similar to Mycoplasma | Part of the human vaginal and lower urinary tract
microbiota; may cause inflammation, sometimes leading to
internal scarring and infertility | \n**Table 4.10** \n \n- Name some ways in which streptococci are classified.\n- Name one pathogenic low G+C gram-positive bacterium and a disease it causes. \n#### **Clinical Focus** \n#### **Resolution** \nMarsha's sputum sample was sent to the microbiology lab to confirm the identity of the microorganism causing her infection. The lab also performed antimicrobial susceptibility testing (AST) on the sample to confirm that the physician has prescribed the correct antimicrobial drugs. \nDirect microscopic examination of the sputum revealed acid-fast bacteria (AFB) present in Marsha's sputum. When placed in culture, there were no signs of growth for the first 8 days, suggesting that microorganism was either dead or growing very slowly. Slow growth is a distinctive characteristic of *M. tuberculosis*. \nAfter four weeks, the lab microbiologist observed distinctive colorless granulated colonies (**[Figure 4.23](#page-191-0)**). The colonies contained AFB showing the same microscopic characteristics as those revealed during the direct microscopic examination of Marsha's sputum. To confirm the identification of the AFB, samples of the colonies were analyzed using nucleic acid hybridization, or direct nucleic acid amplification (NAA) testing. When a bacterium is acid-fast, it is classified in the family *Mycobacteriaceae*. DNA sequencing of variable genomic regions of the DNA extracted from these bacteria revealed that it was high G+C. This fact served to finalize Marsha's diagnosis as infection with *M. tuberculosis*. After nine months of treatment with the drugs prescribed by her doctor, Marsha made a full recovery. \n \n**Figure 4.23** *M. tuberculosis* grows on Löwenstein-Jensen (LJ) agar in distinct colonies. (credit: Centers for Disease Control and Prevention) \n*Go back to the [previous](#page-185-0) Clinical Focus box.* \n#### **Eye on Ethics** \n \n#### **Biopiracy and Bioprospecting** \nIn 1969, an employee of a Swiss pharmaceutical company was vacationing in Norway and decided to collect some soil samples. He took them back to his lab, and the Swiss company subsequently used the fungus *Tolypocladium inflatum* in those samples to develop cyclosporine A, a drug widely used in patients who undergo tissue or organ transplantation. The Swiss company earns more than \\$1 billion a year for production of cyclosporine A, yet Norway receives nothing in return—no payment to the government or benefit for the Norwegian people. Despite the fact the cyclosporine A saves numerous lives, many consider the means by which the soil samples were obtained to be an act of \"biopiracy,\" essentially a form of theft. Do the ends justify the means in a case like this? \nNature is full of as-yet-undiscovered bacteria and other microorganisms that could one day be used to develop new life-saving drugs or treatments.[21] Pharmaceutical and biotechnology companies stand to reap huge profits from such discoveries, but ethical questions remain. To whom do biological resources belong? Should companies who invest (and risk) millions of dollars in research and development be required to share revenue or royalties for the right to access biological resources? \nCompensation is not the only issue when it comes to bioprospecting. Some communities and cultures are philosophically opposed to bioprospecting, fearing unforeseen consequences of collecting genetic or biological material. Native Hawaiians, for example, are very protective of their unique biological resources. \nFor many years, it was unclear what rights government agencies, private corporations, and citizens had when it came to collecting samples of microorganisms from public land. Then, in 1993, the Convention on Biological Diversity granted each nation the rights to any genetic and biological material found on their own land. Scientists can no longer collect samples without a prior arrangement with the land owner for compensation. This convention now ensures that companies act ethically in obtaining the samples they use to create their products.",
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"page_content": "#### **Learning Objectives** \n- Describe the unique features of deeply branching bacteria\n- Give examples of significant deeply branching bacteria \nOn a phylogenetic tree (see **[A Systematic Approach](#page-32-0)**), the trunk or root of the tree represents a common ancient evolutionary ancestor, often called the last universal common ancestor (LUCA), and the branches are its evolutionary descendants. Scientists consider the **deeply branching bacteria**, such as the genus *Acetothermus*, to be the first of these non-LUCA forms of life produced by evolution some 3.5 billion years ago. When placed on the phylogenetic tree, they stem from the common root of life, deep and close to the LUCA root—hence the name \"deeply branching\" (**[Figure 4.24](#page-192-1)**). \n**Figure 4.24** The star on this phylogenetic tree of life shows the position of the deeply branching bacteria *Acetothermus*. (credit: modification of work by Eric Gaba) \nThe deeply branching bacteria may provide clues regarding the structure and function of ancient and now extinct forms of life. We can hypothesize that ancient bacteria, like the deeply branching bacteria that still exist, were thermophiles or hyperthermophiles, meaning that they thrived at very high temperatures. *Acetothermus paucivorans*, a gram-negative anaerobic bacterium discovered in 1988 in sewage sludge, is a thermophile growing at an optimal temperature of 58 °C.[22] Scientists have determined it to be the deepest branching bacterium, or the closest evolutionary relative of the LUCA (**[Figure 4.24](#page-192-1)**). \nThe class Aquificae includes deeply branching bacteria that are adapted to the harshest conditions on our planet, resembling the conditions thought to dominate the earth when life first appeared. Bacteria from the genus *Aquifex* \n21. J. Andre. *Bioethics as Practice*. Chapel Hill, NC: University of North Carolina Press, 2002. \n22. G. Dietrich et al. \"*Acetothermus paucivorans*, gen. nov., sp. Nov., a Strictly Anaerobic, Thermophilic Bacterium From Sewage Sludge, Fermenting Hexoses to Acetate, CO2 , and H2 .\" *Systematic and Applied Microbiology* 10 no. 2 (1988):174–179. \nare hyperthermophiles, living in hot springs at a temperature higher than 90 °C. The species *A. pyrophilus* thrives near underwater volcanoes and thermal ocean vents, where the temperature of water (under high pressure) can reach 138 °C. *Aquifex* bacteria use inorganic substances as nutrients. For example, *A. pyrophilus* can reduce oxygen, and it is able to reduce nitrogen in anaerobic conditions. They also show a remarkable resistance to ultraviolet light and ionizing radiation. Taken together, these observations support the hypothesis that the ancient ancestors of deeply branching bacteria began evolving more than 3 billion years ago, when the earth was hot and lacked an atmosphere, exposing the bacteria to nonionizing and ionizing radiation. \nThe class Thermotogae is represented mostly by hyperthermophilic, as well as some mesophilic (preferring moderate temperatures), anaerobic gram-negative bacteria whose cells are wrapped in a peculiar sheath-like outer membrane called a toga. The thin layer of peptidoglycan in their cell wall has an unusual structure; it contains diaminopimelic acid and D-lysine. These bacteria are able to use a variety of organic substrates and produce molecular hydrogen, which can be used in industry. The class contains several genera, of which the best known is the genus *Thermotoga*. One species of this genus, *T. maritima*, lives near the thermal ocean vents and thrives in temperatures of 90 °C; another species, *T. subterranea*, lives in underground oil reservoirs. \nFinally, the deeply branching bacterium *Deinococcus radiodurans* belongs to a genus whose name is derived from a Greek word meaning *terrible berry*. Nicknamed \"Conan the Bacterium,\" *D. radiodurans* is considered a polyextremophile because of its ability to survive under the many different kinds of extreme conditions—extreme heat, drought, vacuum, acidity, and radiation. It owes its name to its ability to withstand doses of ionizing radiation that kill all other known bacteria; this special ability is attributed to some unique mechanisms of DNA repair. \n \n**Figure 4.25** *Deinococcus radiodurans*, or \"Conan the Bacterium,\" survives in the harshest conditions on earth.",
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"page_content": "#### **Learning Objectives** \n- Describe the unique features of each category of Archaea\n- Explain why archaea might not be associated with human microbiomes or pathology\n- Give common examples of archaea commonly associated with unique environmental habitats \nLike organisms in the domain Bacteria, organisms of the domain **Archaea** are all unicellular organisms. However, archaea differ structurally from bacteria in several significant ways, as discussed in **[Unique Characteristics of](#page-111-0)** \n#### **[Prokaryotic Cells](#page-111-0)**. To summarize: \n- The archaeal cell membrane is composed of ether linkages with branched isoprene chains (as opposed to the bacterial cell membrane, which has ester linkages with unbranched fatty acids).\n- Archaeal cell walls lack peptidoglycan, but some contain a structurally similar substance called pseudopeptidoglycan or pseudomurein.\n- The genomes of Archaea are larger and more complex than those of bacteria. \nDomain Archaea is as diverse as domain Bacteria, and its representatives can be found in any habitat. Some archaea are mesophiles, and many are extremophiles, preferring extreme hot or cold, extreme salinity, or other conditions that are hostile to most other forms of life on earth. Their metabolism is adapted to the harsh environments, and they can perform methanogenesis, for example, which bacteria and eukaryotes cannot. \nThe size and complexity of the archaeal genome makes it difficult to classify. Most taxonomists agree that within the Archaea, there are currently five major phyla: Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota. There are likely many other archaeal groups that have not yet been systematically studied and classified. \nWith few exceptions, archaea are not present in the human microbiota, and none are currently known to be associated with infectious diseases in humans, animals, plants, or microorganisms. However, many play important roles in the environment and may thus have an indirect impact on human health. \n#### **Crenarchaeota** \nCrenarchaeota is a class of Archaea that is extremely diverse, containing genera and species that differ vastly in their morphology and requirements for growth. All Crenarchaeota are aquatic organisms, and they are thought to be the most abundant microorganisms in the oceans. Most, but not all, Crenarchaeota are hyperthermophiles; some of them (notably, the genus *Pyrolobus*) are able to grow at temperatures up to 113 °C.[23] \nArchaea of the genus *Sulfolobus* (**[Figure 4.26](#page-195-0)**) are thermophiles that prefer temperatures around 70–80°C and acidophiles that prefer a pH of 2–3.[24] *Sulfolobus* can live in aerobic or anaerobic environments. In the presence of oxygen, *Sulfolobus* spp. use metabolic processes similar to those of heterotrophs. In anaerobic environments, they oxidize sulfur to produce sulfuric acid, which is stored in granules. *Sulfolobus* spp. are used in biotechnology for the production of thermostable and acid-resistant proteins called affitins.[25] Affitins can bind and neutralize various antigens (molecules found in toxins or infectious agents that provoke an immune response from the body). \n23. E. Blochl et al.\"*Pyrolobus fumani*, gen. and sp. nov., represents a novel group of Archaea, extending the upper temperature limit for life to 113°C.\" *Extremophiles* 1 (1997):14–21. \n24. T.D. Brock et al. \"*Sulfolobus*: A New Genus of Sulfur-Oxidizing Bacteria Living at Low pH and High Temperature.\" *Archiv für Mikrobiologie* 84 no. 1 (1972):54–68. \n25. S. Pacheco et al. \"Affinity Transfer to the Archaeal Extremophilic Sac7d Protein by Insertion of a CDR.\" *Protein Engineering Design and Selection* 27 no. 10 (2014):431-438. \n \n**Figure 4.26** *Sulfolobus*, an archaeon of the class Crenarchaeota, oxidizes sulfur and stores sulfuric acid in its granules. \nAnother genus, *Thermoproteus*, is represented by strictly anaerobic organisms with an optimal growth temperature of 85 °C. They have flagella and, therefore, are motile. *Thermoproteus* has a cellular membrane in which lipids form a monolayer rather than a bilayer, which is typical for archaea. Its metabolism is autotrophic. To synthesize ATP, *Thermoproteus* spp. reduce sulfur or molecular hydrogen and use carbon dioxide or carbon monoxide as a source of carbon. *Thermoproteus* is thought to be the deepest-branching genus of Archaea, and thus is a living example of some of our planet's earliest forms of life. \n \n• What types of environments do Crenarchaeota prefer?\n\nThe phylum Euryarchaeota includes several distinct classes. Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane. They can live in the most extreme environments and can reproduce at temperatures varying from below freezing to boiling. Methanogens have been found in hot springs as well as deep under ice in Greenland. Some scientists have even hypothesized that **methanogens** may inhabit the planet Mars because the mixture of gases produced by methanogens resembles the makeup of the Martian atmosphere.[26] \nMethanogens are thought to contribute to the formation of anoxic sediments by producing hydrogen sulfide, making \"marsh gas.\" They also produce gases in ruminants and humans. Some genera of methanogens, notably *Methanosarcina*, can grow and produce methane in the presence of oxygen, although the vast majority are strict anaerobes. \nThe class Halobacteria (which was named before scientists recognized the distinction between Archaea and Bacteria) includes halophilic (\"salt-loving\") archaea. Halobacteria require a very high concentrations of sodium chloride in their aquatic environment. The required concentration is close to saturation, at 36%; such environments include the Dead Sea as well as some salty lakes in Antarctica and south-central Asia. One remarkable feature of these organisms \n26. R.R. Britt \"Crater Critters: Where Mars Microbes Might Lurk.\" http://www.space.com/1880-crater-critters-mars-microbes-lurk.html. Accessed April 7, 2015. \nChapter 4 | Prokaryotic Diversity 187 \nis that they perform photosynthesis using the protein bacteriorhodopsin, which gives them, and the bodies of water they inhabit, a beautiful purple color (**[Figure 4.27](#page-196-0)**). \n \n**Figure 4.27** Halobacteria growing in these salt ponds gives them a distinct purple color. (credit: modification of work by Tony Hisgett) \nNotable species of Halobacteria include *Halobacterium salinarum*, which may be the oldest living organism on earth; scientists have isolated its DNA from fossils that are 250 million years old.[27] Another species, *Haloferax volcanii*, shows a very sophisticated system of ion exchange, which enables it to balance the concentration of salts at high temperatures. \n \n• Where do Halobacteria live? \n#### **Micro Connections** \n#### **Finding a Link Between Archaea and Disease** \nArchaea are not known to cause any disease in humans, animals, plants, bacteria, or in other archaea. Although this makes sense for the extremophiles, not all archaea live in extreme environments. Many genera and species of Archaea are mesophiles, so they can live in human and animal microbiomes, although they rarely do. As we have learned, some methanogens exist in the human gastrointestinal tract. Yet we have no reliable evidence pointing to any archaean as the causative agent of any human disease. \nStill, scientists have attempted to find links between human disease and archaea. For example, in 2004, Lepp et al. presented evidence that an archaean called *Methanobrevibacter oralis* inhabits the gums of patients with periodontal disease. The authors suggested that the activity of these methanogens causes the disease.[28] However, it was subsequently shown that there was no causal relationship between *M. oralis* and periodontitis. It seems more likely that periodontal disease causes an enlargement of anaerobic regions in the mouth that are subsequently populated by *M. oralis*. [29] \n- 27. H. Vreeland et al. \"Fatty acid and DA Analyses of Permian Bacterium Isolated From Ancient Salt Crystals Reveal Differences With Their Modern Relatives.\" *Extremophiles* 10 (2006):71–78.\n- 28. P.W. Lepp et al. \"Methanogenic Archaea and Human Gum Disease.\" *Proceedings of the National Academies of Science of the United* \nThere remains no good answer as to why archaea do not seem to be pathogenic, but scientists continue to speculate and hope to find the answer. \n#### **Summary** \n#### **[4.1 Prokaryote Habitats, Relationships, and Microbiomes](#page-159-0)** \n- Prokaryotes are unicellular microorganisms whose cells have no nucleus.\n- Prokaryotes can be found everywhere on our planet, even in the most extreme environments.\n- Prokaryotes are very flexible metabolically, so they are able to adjust their feeding to the available natural resources.\n- Prokaryotes live in **communities** that interact among themselves and with large organisms that they use as hosts (including humans).\n- The totality of forms of prokaryotes (particularly bacteria) living on the human body is called the human microbiome, which varies between regions of the body and individuals, and changes over time.\n- The totality of forms of prokaryotes (particularly bacteria) living in a certain region of the human body (e.g., mouth, throat, gut, eye, vagina) is called the **microbiota** of this region.\n- Prokaryotes are classified into domains Archaea and Bacteria.\n- In recent years, the traditional approaches to classification of prokaryotes have been supplemented by approaches based on molecular genetics. \n#### **[4.2 Proteobacteria](#page-166-0)** \n- **Proteobacteria** is a phylum of gram-negative bacteria discovered by Carl Woese in the 1980s based on nucleotide sequence homology.\n- Proteobacteria are further classified into the classes alpha-, beta-, gamma-, delta- and epsilonproteobacteria, each class having separate orders, families, genera, and species.\n- **Alphaproteobacteria** are **oligotrophs**. The taxa chlamydias and rickettsias are **obligate intracellular pathogens,** feeding on cells of host organisms; they are metabolically inactive outside of the host cell. Some Alphaproteobacteria can convert atmospheric nitrogen to nitrites, making nitrogen usable by other forms of life.\n- **Betaproteobacteria** are **eutrophs**. They include human pathogens of the genus *Neisseria* and the species *Bordetella pertussis*.\n- **Gammaproteobacteria** are the largest and the most diverse group of Proteobacteria. Many are human pathogens that are aerobes or facultative anaerobes. Some Gammaproteobacteria are **enteric** bacteria that may be coliform or noncoliform. *Escherichia coli*, a member of Gammaproteobacteria, is perhaps the most studied bacterium.\n- **Deltaproteobacteria** make up a small group able to reduce sulfate or elemental sulfur. Some are scavengers and form myxospores, with multicellular fruiting bodies.\n- **Epsilonproteobacteria** make up the smallest group of Proteobacteria. The genera *Campylobacter* and *Helicobacter* are human pathogens. \n#### **[4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria](#page-176-0)** \n- Gram-negative nonproteobacteria include the taxa **spirochetes**; the *Cytophaga*, *Fusobacterium*, *Bacteroides* group; Planctomycetes; and many representatives of **phototrophic bacteria.**\n- Spirochetes are motile, spiral bacteria with a long, narrow body; they are difficult or impossible to culture. \n*States of America* 101 no. 16 (2004):6176–6181. \n29. R.I. Aminov. \"Role of Archaea in Human Disease.\" *Frontiers in Cellular and Infection Microbiology* 3 (2013):42. \n- Several genera of spirochetes contain human pathogens that cause such diseases as syphilis and Lyme disease.\n- *Cytophaga*, *Fusobacterium*, and *Bacteroides* are classified together as a phylum called the **CFB group**. They are rod-shaped anaerobic organoheterotrophs and avid fermenters. *Cytophaga* are aquatic bacteria with the gliding motility. *Fusobacteria* inhabit the human mouth and may cause severe infectious diseases. *Bacteroides* are present in vast numbers in the human gut, most of them being mutualistic but some are pathogenic.\n- Planctomycetes are aquatic bacteria that reproduce by budding; they may form large colonies, and develop a holdfast.\n- Phototrophic bacteria are not a taxon but, rather, a group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.\n- Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.\n- Some phototrophic bacteria are able to fix nitrogen, providing the usable forms of nitrogen to other organisms.\n- **Cyanobacteria** are oxygen-producing bacteria thought to have played a critical role in the forming of the earth's atmosphere. \n#### **[4.4 Gram-Positive Bacteria](#page-182-0)** \n- Gram-positive bacteria are a very large and diverse group of microorganisms. Understanding their taxonomy and knowing their unique features is important for diagnostics and treatment of infectious diseases.\n- Gram-positive bacteria are classified into **high G+C gram-positive** and **low G+C gram-positive** bacteria, based on the prevalence of guanine and cytosine nucleotides in their genome\n- Actinobacteria is the taxonomic name of the class of high G+C gram-positive bacteria. This class includes the genera *Actinomyces, Arthrobacter, Corynebacterium, Frankia, Gardnerella, Micrococcus, Mycobacterium, Nocardia*, *Propionibacterium, Rhodococcus,* and *Streptomyces*. Some representatives of these genera are used in industry; others are human or animal pathogens.\n- Examples of high G+C gram-positive bacteria that are human pathogens include *Mycobacterium tuberculosis*, which causes tuberculosis; *M. leprae*, which causes leprosy (Hansen's disease); and *Corynebacterium diphtheriae*, which causes diphtheria.\n- *Clostridia* spp. are low G+C gram-positive bacteria that are generally obligate anaerobes and can form endospores. Pathogens in this genus include *C. perfringens* (gas gangrene), *C. tetani* (tetanus), and *C. botulinum* (botulism).\n- Lactobacillales include the genera *Enterococcus*, *Lactobacillus*, *Leuconostoc*, and *Streptococcus. Streptococcus* is responsible for many human diseases, including pharyngitis (strep throat), scarlet fever, rheumatic fever, glomerulonephritis, pneumonia, and other respiratory infections.\n- Bacilli is a taxonomic class of low G+C gram-positive bacteria that include rod-shaped and coccus-shaped species, including the genera *Bacillus* and *Staphylococcus*. *B. anthracis* causes anthrax, *B. cereus* may cause opportunistic infections of the gastrointestinal tract, and *S. aureus* strains can cause a wide range of infections and diseases, many of which are highly resistant to antibiotics.\n- *Mycoplasma* spp. are very small, **pleomorphic** low G+C gram-positive bacteria that lack cell walls. *M. pneumoniae* causes atypical pneumonia. \n#### **[4.5 Deeply Branching Bacteria](#page-192-0)** \n- **Deeply branching bacteria** are phylogenetically the most ancient forms of life, being the closest to the last universal common ancestor.\n- Deeply branching bacteria include many species that thrive in extreme environments that are thought to resemble conditions on earth billions of years ago\n- Deeply branching bacteria are important for our understanding of evolution; some of them are used in industry \n#### **[4.6 Archaea](#page-193-0)** \n• **Archaea** are unicellular, prokaryotic microorganisms that differ from bacteria in their genetics, biochemistry, \n- and ecology.\n- Some archaea are extremophiles, living in environments with extremely high or low temperatures, or extreme salinity.\n- Only archaea are known to produce methane. Methane-producing archaea are called **methanogens**.\n- Halophilic archaea prefer a concentration of salt close to saturation and perform photosynthesis using bacteriorhodopsin.\n- Some archaea, based on fossil evidence, are among the oldest organisms on earth.\n- Archaea do not live in great numbers in human microbiomes and are not known to cause disease.",
"metadata": {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "Archaea",
"is_merged_section": true,
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
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"page_content": " \n**Figure 1.1** A veterinarian gets ready to clean a sea turtle covered in oil following the Deepwater Horizon oil spill in the Gulf of Mexico in 2010. After the spill, the population of a naturally occurring oil-eating marine bacterium called *Alcanivorax borkumensis* skyrocketed, helping to get rid of the oil. Scientists are working on ways to genetically engineer this bacterium to be more efficient in cleaning up future spills. (credit: modification of work by NOAA's National Ocean Service) \n#### **Chapter Outline** \n- [1.1 What Our Ancestors Knew](#page-25-0)\n- [1.2 A Systematic Approach](#page-32-0)\n- [1.3 Types of Microorganisms](#page-38-0)",
"metadata": {
"Header 1": "**An Invisible World**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
},
{
"page_content": " \n**40.** Contrast the behavior of a virus outside versus inside a cell. \n",
"metadata": {
"Header 1": "**An Invisible World**",
"Header 2": "**39.** Label the three Domains found on modern phylogenetic trees.",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
},
{
"page_content": " \n**Figure 2.1** Different types of microscopy are used to visualize different structures. Brightfield microscopy (left) renders a darker image on a lighter background, producing a clear image of these *Bacillus anthracis* cells in cerebrospinal fluid (the rod-shaped bacterial cells are surrounded by larger white blood cells). Darkfield microscopy (right) increases contrast, rendering a brighter image on a darker background, as demonstrated by this image of the bacterium *Borrelia burgdorferi*, which causes Lyme disease. (credit left: modification of work by Centers for Disease Control and Prevention; credit right: modification of work by American Society for Microbiology) \n#### **Chapter Outline** \n- [2.1 The Properties of Light](#page-53-0)\n- [2.2 Peering Into the Invisible World](#page-59-0)\n- [2.3 Instruments of Microscopy](#page-62-0)\n- [2.4 Staining Microscopic Specimens](#page-80-0)",
"metadata": {
"Header 1": "**How We See the Invisible World**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
},
{
"page_content": "When we look at a rainbow, its colors span the full spectrum of light that the human eye can detect and differentiate. Each hue represents a different frequency of visible light, processed by our eyes and brains and rendered as red, orange, yellow, green, or one of the many other familiar colors that have always been a part of the human experience. But only recently have humans developed an understanding of the properties of light that allow us to see images in color. \nOver the past several centuries, we have learned to manipulate light to peer into previously invisible worlds—those too small or too far away to be seen by the naked eye. Through a microscope, we can examine microbial cells and colonies, using various techniques to manipulate color, size, and contrast in ways that help us identify species and diagnose disease. \n**[Figure 2.1](#page-52-1)** illustrates how we can apply the properties of light to visualize and magnify images; but these stunning micrographs are just two examples of the numerous types of images we are now able to produce with different microscopic technologies. This chapter explores how various types of microscopes manipulate light in order to provide a window into the world of microorganisms. By understanding how various kinds of microscopes work, we can produce highly detailed images of microbes that can be useful for both research and clinical applications.",
"metadata": {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Introduction**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
},
{
"page_content": " \nRead this **[article \\(https://www.openstax.org/l/22aperture\\)](https://www.openstax.org/l/22aperture)** to learn more about factors that can increase or decrease the numerical aperture of a lens. \nEven when a microscope has high resolution, it can be difficult to distinguish small structures in many specimens \nbecause microorganisms are relatively transparent. It is often necessary to increase **contrast** to detect different structures in a specimen. Various types of microscopes use different features of light or electrons to increase contrast—visible differences between the parts of a specimen (see **[Instruments of Microscopy](#page-62-0)**). Additionally, dyes that bind to some structures but not others can be used to improve the contrast between images of relatively transparent objects (see **[Staining Microscopic Specimens](#page-80-0)**). \n \n- Explain the difference between magnification and resolution.\n- Explain the difference between resolution and contrast.\n- Name two factors that affect resolution.",
"metadata": {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.1 The Properties of Light**",
"Header 3": "**Link to Learning**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
},
{
"page_content": " \n**Figure 4.1** The bacterium *Shewanella* lives in the deep sea, where there is little oxygen diffused in the water. It is able to survive in this harsh environment by attaching to the sea floor and using long appendages, called \"nanocables,\" to sense oxygen. (credit a: modification of work by NASA; credit b: modification of work by Liza Gross) \n#### **Chapter Outline** \n- [4.1 Prokaryote Habitats, Relationships, and Microbiomes](#page-159-0)\n- [4.2 Proteobacteria](#page-166-0)\n- [4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria](#page-176-0)\n- [4.4 Gram-Positive Bacteria](#page-182-0)\n- [4.5 Deeply Branching Bacteria](#page-192-0)\n- [4.6 Archaea](#page-193-0)",
"metadata": {
"Header 1": "**Prokaryotic Diversity**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
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{
"page_content": "Scientists have studied prokaryotes for centuries, but it wasn't until 1966 that scientist Thomas Brock (1926–) discovered that certain bacteria can live in boiling water. This led many to wonder whether prokaryotes may also live in other extreme environments, such as at the bottom of the ocean, at high altitudes, or inside volcanoes, or even on other planets. \nProkaryotes have an important role in changing, shaping, and sustaining the entire biosphere. They can produce proteins and other substances used by molecular biologists in basic research and in medicine and industry. For example, the bacterium *Shewanella* lives in the deep sea, where oxygen is scarce. It grows long appendages, which have special sensors used to seek the limited oxygen in its environment. It can also digest toxic waste and generate electricity. Other species of prokaryotes can produce more oxygen than the entire Amazon rainforest, while still others supply plants, animals, and humans with usable forms of nitrogen; and inhabit our body, protecting us from harmful microorganisms and producing some vitally important substances. This chapter will examine the diversity, structure, and function of prokaryotes.",
"metadata": {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Introduction**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
},
{
"page_content": "Assigning prokaryotes to a certain species is challenging. They do not reproduce sexually, so it is not possible to classify them according to the presence or absence of interbreeding. Also, they do not have many morphological features. Traditionally, the classification of prokaryotes was based on their shape, staining patterns, and biochemical or physiological differences. More recently, as technology has improved, the nucleotide sequences in genes have become an important criterion of microbial classification. \nIn 1923, American microbiologist David Hendricks Bergey (1860–1937) published *A Manual in Determinative Bacteriology.* With this manual, he attempted to summarize the information about the kinds of bacteria known at that time, using Latin binomial classification. Bergey also included the morphological, physiological, and biochemical properties of these organisms. His manual has been updated multiple times to include newer bacteria and their properties. It is a great aid in bacterial taxonomy and methods of characterization of bacteria. A more recent sister publication, the five-volume *Bergey's Manual of Systematic Bacteriology*, expands on Bergey's original manual. It includes a large number of additional species, along with up-to-date descriptions of the taxonomy and biological properties of all named prokaryotic taxa. This publication incorporates the approved names of bacteria as determined by the List of Prokaryotic Names with Standing in Nomenclature (LPSN). \n#### **Link to Learning** \n \n*Bergey's Manual of Determinative Bacteriology* is now **[available](https://openstax.org/l/22mandeterbact) [\\(https://openstax.org/l/22mandeterbact\\)](https://openstax.org/l/22mandeterbact)** online. You can also access a searchable **[database \\(https://openstax.org/l/22databmicrefst\\)](https://openstax.org/l/22databmicrefst)** of microbial reference strains, published by the American Type Culture Collection (ATCC). \n#### **Classification by Staining Patterns** \nAccording to their staining patterns, which depend on the properties of their cell walls, bacteria have traditionally been classified into gram-positive, gram-negative, and \"atypical,\" meaning neither gram-positive nor gram-negative. As explained in **[Staining Microscopic Specimens](#page-80-0)**, gram-positive bacteria possess a thick peptidoglycan cell wall that retains the primary stain (crystal violet) during the decolorizing step; they remain purple after the gramstain procedure because the crystal violet dominates the light red/pink color of the secondary counterstain, safranin. In contrast, gram-negative bacteria possess a thin peptidoglycan cell wall that does not prevent the crystal violet from washing away during the decolorizing step; therefore, they appear light red/pink after staining with the safranin. Bacteria that cannot be stained by the standard Gram stain procedure are called atypical bacteria. Included in the atypical category are species of *Mycoplasma* and *Chlamydia*, which lack a cell wall and therefore cannot retain the gram-stain reagents. *Rickettsia* are also considered atypical because they are too small to be evaluated by the Gram stain. \nMore recently, scientists have begun to further classify gram-negative and gram-positive bacteria. They have added a special group of deeply branching bacteria based on a combination of physiological, biochemical, and genetic features. They also now further classify gram-negative bacteria into Proteobacteria, *Cytophaga-Flavobacterium-Bacteroides* (CFB), and spirochetes. \nThe deeply branching bacteria are thought to be a very early evolutionary form of bacteria (see **[Deeply Branching](#page-192-0) [Bacteria](#page-192-0)**). They live in hot, acidic, ultraviolet-light-exposed, and anaerobic (deprived of oxygen) conditions. Proteobacteria is a phylum of very diverse groups of gram-negative bacteria; it includes some important human pathogens (e.g., *E. coli* and *Bordetella pertussis*). The CFB group of bacteria includes components of the normal human gut microbiota, like *Bacteroides*. The spirochetes are spiral-shaped bacteria and include the pathogen *Treponema pallidum*, which causes syphilis. We will characterize these groups of bacteria in more detail later in the chapter. \nBased on their prevalence of guanine and cytosine nucleotides, gram-positive bacteria are also classified into low G+C and high G+C gram-positive bacteria. The low G+C gram-positive bacteria have less than 50% of guanine and cytosine nucleotides in their DNA. They include human pathogens, such as those that cause anthrax (*Bacillus anthracis*), tetanus (*Clostridium tetani*), and listeriosis (*Listeria monocytogenes*). High G+C gram-positive bacteria, which have more than 50% guanine and cytosine nucleotides in their DNA, include the bacteria that cause diphtheria (*Corynebacterium diphtheriae*), tuberculosis (*Mycobacterium tuberculosis*), and other diseases. \nThe classifications of prokaryotes are constantly changing as new species are being discovered. We will describe them in more detail, along with the diseases they cause, in later sections and chapters. \n \n• How do scientists classify prokaryotes? \n#### **Micro Connections** \n#### **Human Microbiome Project** \nThe Human Microbiome Project was launched by the National Institutes of Health (NIH) in 2008. One main goal of the project is to create a large repository of the gene sequences of important microbes found in humans, helping biologists and clinicians understand the dynamics of the human microbiome and the relationship between the human microbiota and diseases. A network of labs working together has been compiling the data from swabs of several areas of the skin, gut, and mouth from hundreds of individuals. \nOne of the challenges in understanding the human microbiome has been the difficulty of culturing many of the microbes that inhabit the human body. It has been estimated that we are only able to culture 1% of the bacteria in nature and that we are unable to grow the remaining 99%. To address this challenge, researchers have used metagenomic analysis, which studies genetic material harvested directly from microbial communities, as opposed to that of individual species grown in a culture. This allows researchers to study the genetic material of all microbes in the microbiome, rather than just those that can be cultured.[6] \nOne important achievement of the Human Microbiome Project is establishing the first reference database on microorganisms living in and on the human body. Many of the microbes in the microbiome are beneficial, but some are not. It was found, somewhat unexpectedly, that all of us have some serious microbial pathogens in our microbiota. For example, the conjunctiva of the human eye contains 24 genera of bacteria and numerous pathogenic species.[7] A healthy human mouth contains a number of species of the genus *Streptococcus*, including pathogenic species *S. pyogenes* and *S. pneumoniae*. [8] This raises the question of why certain prokaryotic organisms exist commensally in certain individuals but act as deadly pathogens in others. Also unexpected was the number of organisms that had never been cultured. For example, in one metagenomic study of the human gut microbiota, 174 new species of bacteria were identified.[9] \nAnother goal for the near future is to characterize the human microbiota in patients with different diseases and to find out whether there are any relationships between the contents of an individual's microbiota and risk for or susceptibility to specific diseases. Analyzing the microbiome in a person with a specific disease may reveal new ways to fight diseases. \n- 6. National Institutes of Health. \"Human Microbiome Project. Overview.\" http://commonfund.nih.gov/hmp/overview. Accessed June 7, 2016.\n- 7. Q. Dong et al. \"Diversity of Bacteria at Healthy Human Conjunctiva.\" *Investigative Ophthalmology & Visual Science* 52 no. 8 (2011):5408–5413.\n- 8. F.E. Dewhirst et al. \"The Human Oral Microbiome.\" *Journal of Bacteriology* 192 no. 19 (2010):5002–5017.\n- 9. J.C. Lagier et al. \"Microbial Culturomics: Paradigm Shift in the Human Gut Microbiome Study.\" *Clinical Microbiology and Infection* 18 no. 12 (2012):1185–1193.",
"metadata": {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Symbiotic Relationships**",
"Header 3": "**Taxonomy and Systematics**",
"source_pdf": "/share/project/bs_scaling/lmse/self-evolution-explore/datasets/websources/Bio/Microbiology-LR.pdf"
}
}
]