Chapter 1 Outline PDF

I.​ Introduction A.​ Microorganisms (aka microbes) are small organisms that can be found almost everywhere on earth in great quantities. Most are so small they cannot be seen with the human eye. B.​ Most microbes are harmless to humans, and many are helpful living on or inside of the...

I.​ Introduction A.​ Microorganisms (aka microbes) are small organisms that can be found almost everywhere on earth in great quantities. Most are so small they cannot be seen with the human eye. B.​ Most microbes are harmless to humans, and many are helpful living on or inside of the human body. C.​ Microbes play fundamental roles in ecosystems everywhere on earth, forming the backbone of many food webs, we use them in biofuels, medicine, and food. D.​ Much is still left to learn about this fascinating field. II.​ 1.1 What Our Ancestor’s Knew A.​ A few hundred years ago, before the invention of the microscope, the existence of many types of microbes was impossible to prove. Microorganisms (aka 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. 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. B.​ Fermented Foods and Beverages 1.​ People across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. 2.​ The people in Neolithic China made a fermented beverage from rice, honey, and fruit as early as 7000 BC. 3.​ Production 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 C.​ The Iceman Treateth 1.​ Prehistoric people attempted to treat illnesses and infections. 2.​ Ex: Ötzi the Iceman, a 5300-year-old mummy found frozen in the ice of the Ötzal Alps on the Austrian-Italian border in 1991. a.​ 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. b.​ Researchers also found evidence of Borrelia burgdorferi, a bacterium that causes Lyme disease. c.​ 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. This fungus has both laxative and antibiotic properties. d.​ Ötzi was also covered in tattoos that were made by cutting incisions into his skin, filling them with herbs, and then burning the herbs. There is speculation that this may have been another attempt to treat his health ailments. D.​ Early Notions of Disease, Contagion, and Containment 1.​ Several ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. 2.​ The Bible refers to the practice of quarantining people with leprosy and other diseases, suggesting that people understood that diseases could be communicable. 3.​ The ancient Greeks attributed disease to bad air, mal’aria, which they called “miasmatic odors.” They developed hygiene practices that built on this idea. 4.​ 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. Some researchers believe that this infrastructure helped protect the Romans from epidemics of waterborne illnesses. 5.​ 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. a.​ The Greek physician Hippocrates (460–370 BC) is considered the “father of Western medicine”. He dismissed the idea that disease was caused by supernatural forces and theorized 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. 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. b.​ 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. 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. This observation shows an early understanding of the concept of immunity. c.​ Marcus 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. 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.” E.​ The Birth of Microbiology. The invention of the microscope confirmed existence of the “minute creatures.” 1.​ 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 of rainwater. From his drawings of these little organisms, we now know he was looking at bacteria and protists. 2.​ Nearly 200 years later during the “Golden Age of Microbiology” two famous microbiologists, Louis Pasteur and Robert Koch, were especially active in advancing our understanding of the unseen world of microbes. a.​ Louis 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. b.​ Robert 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). 3.​ 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. F.​ Microbiological Tools. 1.​ 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. 2.​ 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. 3.​ 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. 4.​ 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. 5.​ 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. 6.​ 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. 7.​ An inoculation loop is a handheld tool that ends in a small wire loop. 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. III.​ 1.2 A Systematic Approach. A.​ The Science of Taxonomy. 1.​ Taxonomy - the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. 2.​ The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1701–1778). a.​ Linnaeus published Systema Naturae an 11-page booklet in which he used a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. b.​ Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral. 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. B.​ Evolving Trees of Life (Phylogenies). 1.​ 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. 2.​ In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms. He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria. 3.​ Nearly 100 years later, in 1969, American ecologist Robert Whittaker (1920–1980) proposed adding another kingdom—Fungi—in his tree of life. a.​ 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). b.​ Empire Prokaryota contained just the Kingdom Monera. c.​ The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. d.​ Whittaker’s five-kingdom tree was considered the standard phylogeny for many years. C.​ The Role of Genetics in Modern Taxonomy. 1.​ 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. 2.​ American microbiologists Carl Woese and George Fox created a genetics-based tree of life based on similarities and differences they observed in the gene sequences coding for small subunit ribosomal RNA (rRNA) of different organisms. Analysis of small subunit rRNA gene sequences suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. 3.​ Horizontal gene transfer also complicates the issue of classification 4.​ 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. D.​ Naming Microbes.  1.​ Linnaeus used a system of binomial nomenclature, a two-word naming system for identifying organisms by genus and specific epithet. 2.​ Ex: modern humans are in the genus Homo and have the specific epithet 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 specific epithet name, which is not capitalized. Both names are italicized. When referring to the species of humans, the binomial nomenclature would be Homo sapiens. E.​ Bergey’s Manuals is used 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. IV.​ 1.3 Types of Microorganisms A.​ Prokaryotic Microorganisms 1.​ Bacteria are found in nearly every habitat on earth, including within and on humans. a.​ Most bacteria are harmless or helpful, but some are pathogens, causing disease in humans and other animals. b.​ Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. c.​ Most bacteria have cell walls that contain peptidoglycan. d.​ Bacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio). e.​ They have a wide range of metabolic capabilities and can grow in a variety of environments, using different combinations of nutrients. i.​ 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. ii.​ Other types of bacteria are nonphotosynthetic, obtaining their energy from organic or inorganic compounds in their environment. 2.​ 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. a.​ Unlike most bacteria, archaeal cell walls do not contain peptidoglycan, but their cell walls are often composed of a similar substance called pseudopeptidoglycan. b.​ 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. Some archaea live in the human body, but none have been shown to be human pathogens. B.​ Eukaryotic Microorganisms. The 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. 1.​ Protists are an informal grouping of eukaryotes that are not plants, animals, or fungi. a.​ Algae are protists that can be either unicellular or multicellular and vary widely in size, appearance, and habitat. i.​ Their cells are surrounded by cell walls made of cellulose, a type of carbohydrate. ii.​ Algae are photosynthetic organisms that extract energy from the sun and release oxygen and carbohydrates into their environment therefore they are important parts of many ecosystems. iii.​ 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. iv.​ Agar, a gel derived from algae, can be mixed with various nutrients and used to grow microorganisms in a Petri dish. v.​ Algae are also being developed as a possible source for biofuels. b.​ Protozoa are protists that make up the backbone of many food webs by providing nutrients for other organisms. Protozoa are very diverse.  i.​ 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”). ii.​ Some protozoa are photosynthetic; others feed on organic material. iii.​ 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 c.​ Fungi are also eukaryotes. Some multicellular fungi, such as mushrooms, resemble plants, but they are actually quite different. i.​ Fungi are not photosynthetic, and their cell walls are usually made out of chitin rather than cellulose. ii.​ Unicellular 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 uses, 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. iii.​ Multicellular molds are made up of long filaments that form visible colonies. 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. C.​ Helminths are multicellular parasitic worms. 1.​ These worms fall within the field of microbiology because diseases caused by helminths involve microscopic eggs and larvae. 2.​ Ex: 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. 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. D.​ Viruses. 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. E.​ Microbiology as a Field of Study. 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. 1.​ Bacteriology is the study of bacteria. 2.​ Mycology is the study of fungi. 3.​ Protozoology is the study of protozoa. 4.​ Parasitology is the study of helminths and other parasites. 5.​ Virology is the study of viruses. 6.​ 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. 7.​ Microbiologists can also specialize in certain areas of microbiology, such as clinical microbiology, environmental microbiology, applied microbiology, or food microbiology.