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Todar's Online Textbook of Bacteriology Dedication to Hans Zinsser Welcome to Todar's Online Textbook of Bacteriology .This textbook has evolved from lectures presented in my bacteriology courses at the University of Wisconsin-Madison. Its contents are suitable for reading or presentation in...

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Todar's Online Textbook of Bacteriology Dedication to Hans Zinsser

Welcome to Todar's Online Textbook of Bacteriology .This textbook has evolved from lectures presented in my bacteriology courses at the University of Wisconsin-Madison. Its contents are suitable for reading or presentation in courses or course modules concerning general microbiology and medical bacteriology at the college and advanced high school levels of education. As an electronic text, new material is constantly being added, and current material is constantly being revised and updated. This is an inherent advantage of the web-based text over the tree-burner. The textbook will never be complete, as the rate of production of new information in microbiology far outruns the author's ability to acquire and properly present it. If you have suggestions, comments or criticisms regarding the textbook or its contents, or the idea of this type of textbook, please send email to me at the address below. Kenneth Todar University of Wisconsin Department of Bacteriology Madison, Wisconsin 53706

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General Bacteriology Overview of Bacteriology Structure and Function of Procaryotes Nutrition and Growth of Bacteria Growth of Bacterial Populations Control of Microbial Growth The Diversity of Procaryotic Metabolism Regulation and Control of Metabolic Activities Procaryotes in the Environment Important Groups of Procaryotes Bacterial Relationships with Animals The Nature of Host-Parasite Interactions The Bacterial Flora of Humans Mechanisms of Bacterial Pathogenicity Bacteria of Medical Importance The Constitutive Host Defenses The Immune Defenses Principles of Bacterial Pathogenesis Bacterial Structure in Relationship to Pathogenicity Colonization and Invasion by Bacterial Pathogens Bacterial Defense against Phagocytosis Bacterial Defense against Immune Responses Bacterial Protein Toxins Bacterial Endotoxin Antimicrobial Agents Used in the Treatment of Infectious Disease 2

Bacterial Resistance to Antimicrobial Agents Bacterial Pathogens and Diseases of Humans Staphylococcus Streptococcus Streptococcus pneumoniae and Pneumococcal Pneumonia Listeria monocytogenes and Listeriosis Neisseria: Gonorrhea and Meningitis Haemophilus influenzae Opportunistic Infections Caused by Pseudomonas aeruginosa Whooping Cough (Pertussis) E. coli: Gastroenteritis, Urinary Tract Infections and Neonatal Meningitis Cholera Salmonella and Salmonellosis Shigella and Shigellosis Pathogenic Clostridia, including Tetanus and Botulism Bacillus cereus Food Poisoning Bacillus anthracis and Anthrax Diphtheria Tuberculosis Lyme Disease Rickettsial Diseases, including Rocky Mountain Spotted Fever

Emerging Pathogens Vibrio vulnificus

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Important Groups of Procaryotes The Genus Bacillus Pseudomonas and Related Bacteria The Enteric Bacteria

Kenneth Todar is currently on the teaching faculty of the Department of Bacteriology at the University of Wisconsin-Madison. He received a PhD degree from The University of Texas at Austin in 1972. Since 1970, he has taught microbiology at The University of Texas, University of Alaska, and University of Wisconsin. His main teaching interests are in bacterial diversity, microbial ecology and pathogenic bacteriology. Teaching materials associated with three of the courses taught at University of Wisconsin are on the web at Bacteriology 100: The Microbial World Bacteriology 303: Procaryotic Microbiology Bacteriology 330: Host-Parasite Interactions WEB TEXT REVIEW (SCIENCE Magazine VOL 304 04 JUNE 2004 1421) "The Good, the Bad, and the Deadly" "The pearly droplets in this photo are colonies of Bacillus anthracis, the bacterium that causes anthrax. The bugs exude a goopy coating that repels immune system assaults and allows them to establish a foothold in the body. Learn more about the tricks bacteria use to prosper almost everywhere on Earth in this Web text from microbiologist Kenneth Todar of the University of Wisconsin, Madison. High school and college students can absorb the basics of bacterial structure, physiology, classification, and ecology.The book emphasizes medical microbiology, exploring how bacteria hitch a ride from host to host, how the body tries to corral invading microbes, and how the bugs elude these defenses. For example, the cholera bacterium releases a toxin that induces intestinal cells to spill ions and water, producing potentially lethal diarrhea."

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Todar's Online Textbook of Bacteriology

Overview of Bacteriology © 2005 Kenneth Todar University of Wisconsin-Madison Department of Bacteriology The Scope of Bacteriology The Bacteria are a group of single-cell microorganisms with procaryotic cellular configuration. The genetic material (DNA) of procaryotic cells exists unbound in the cytoplasm of the cells. There is no nuclear membrane, which is the definitive characteristic of eukaryotic cells such as those that make up plants and animals. Until recently, bacteria were the only known type of procaryotic cell, and the discipline of biology related to their study is called bacteriology. In the 1980's, with the outbreak of molecular techniques applied to phylogeny of life, another group of procaryotes was defined and informally named "archaebacteria". This group of procaryotes has since been renamed Archaea and has been awarded biological Domain status on the level with Bacteria and Eukarya. The current science of bacteriology includes the study of both Domains of procaryotic cells, but the name "bacteriology" is not likely to change to reflect the inclusion of archaea in the discipline. Actually, many archaea have been studied as intensively and as long as their bacterial counterparts, but with the notion that they were bacteria.

Figure 1. The cyanobacterium Anabaena. American Society for Microbiology. Two (not uncommon) exceptions that procaryotes are unicellular and undifferentiated are seen in Anabaena: 1. The organism lives as a multicellular filament or chain of cells. Procaryotes are considered "unicellular organisms" because all the cells in a filament or colony are of the same type, and any one individual cell can give rise to an exact filament or colony; 2. The predominant photosynthetic (bright yellow-green) cells do differentiate into another type of cell: the obviously large "empty" cells occasionally seen along a filament are differentiated cells in which nitrogen fixation, but not photosynthesis, takes place.

The Origin of Life When life arose on Earth about 4 billion years ago, the first types of cells to evolve were procaryotic cells. For approximately 2 billion years, procaryotic-type cells were the only form of life on Earth. The oldest known sedimentary rocks, from Greenland, are about 3.8 billion years old. The oldest known fossils are procaryotic cells, 3.5 billion years in age, found in Western Australia and South Africa. The nature of these fossils, and the chemical composition of the rocks in which they are found, indicate that lithotrophic and fermentative modes of metabolism were the first to evolve in early procaryotes. Photosynthesis developed in bacteria at least 3 billion years ago. Anoxygenic photosynthesis (bacterial photosynthesis, which is anaerobic and does not produce O2) preceded oxygenic photosynthesis (plant-type photosynthesis, which yields O2). But oxygenic photosynthesis also arose 5

in procaryotes, specifically in the cyanobacteria, which existed millions of years before the evolution of plants. Larger, more complicated eukaryotic cells did not appear until much later, between 1.5 and 2 billion years ago.

Figure 2. Opalescent Pool in Yellowstone National Park, Wyoming USA. K. Todar. Conditions for life in this environment are similar to Earth over 2 billion years ago. In these types of hot springs, the orange, yellow and brown colors are due to pigmented photosynthetic bacteria which make up the microbial mats. The mats are literally teeming with bacteria. Some of these bacteria such as Synechococcus conduct oxygenic photosynthesis, while others such as Chloroflexus conduct anoxygenic photosynthesis. Other non-photosynthetic bacteria, as well as thermophilic and acidophilic Archaea, are also residents of the hot spring community.

The archaea and bacteria differ fundamentally in their cell structure from eukaryotes, which always contain a membrane-enclosed nucleus, multiple chromosomes, and various other membranous organelles, such as mitochondria, chloroplasts, the golgi apparatus, vacuoles, etc. Unlike plants and animals, archaea and bacteria are unicellular organisms that do not develop or differentiate into multicellular forms. Some bacteria grow in filaments or masses of cells, but each cell in the colony is identical and capable of independent existence. The cells may be adjacent to one another because they did not separate after cell division or because they remained enclosed in a common sheath or slime secreted by the cells, but typically there is no continuity or communication between the cells. The Universal Tree of Life On the basis of small subunit ribosomal RNA (ssrRNA) analysis the Woesean tree of life gives rise to three cellular domains of life: Archaea, Bacteria, and Eukarya (Figure 3). Bacteria (formerly known as eubacteria) and Archaea (formerly called archaebacteria) share the procaryotic type of cellular configuration, but otherwise are not related to one another any more closely than they are to the eukaryotic domain, Eukarya. Between the two procaryotes, Archaea are apparently more closely related to Eukarya than are the Bacteria. Eukarya consists of all eukaryotic cell-types, including protista, fungi, plants and animals.

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Figure 3. The Universal Tree of Life as derived from sequencing of ssrRNA. N. Pace. Note the three major domains of living organisms: Archaea, Bacteria and Eucarya (Eukarya). The "evolutionary distance" between two organisms is proportional to the measurable distance between the end of a branch to a node to the end of a comparative branch. For example, in Eucarya, humans (Homo) are more closely related to corn (Zea) than to slime molds (Dictyostelium); or in Bacteria, E. coli is more closely related to Agrobacterium than to Thermus. OFF THE WALL. It is interesting to note several features of phylogeny and evolution that are revealed in the Unrooted Tree. --Archaea are the least evolved type of cell (they remain closest to the common point of origin). This helps explain why contemporary Archaea are inhabitants of environments that are something like the earth 3.86 billion years ago (hot, salty, acidic, anaerobic, low in organic material, etc.). --Eucaryotes (Eucarya) are the most evolved type of cell (they move farthest from the common point of origin). However, the eucaryotes do not begin to diversify (branch) until relatively late in evolution, at a time when the Bacteria diversify into oxygenic photosynthesis (Synechococcus) and aerobic respiration (Agrobacterium). --Mitochondria and the respiratory bacterium, Agrobacterium, are derived from a common ancestor; likewise, chloroplast and the cyanobacterium, Synechococcus, arise from a common origin. This is good evidence for the idea of evolutionary endosymbiosis, i.e., that the origin of eukaryotic mitochondria and chloroplasts is in procaryotic cells that were either captured by, or which invaded, eukaryotic cells, and subsequently entered into a symbiotic association with one cell living inside of the other. --Diversification in Eucarya is within the Protista (unicellular protozoa, algae, and including fungi). The only multicellular eukaryotes on the Tree are Zea (plants) and Homo (animals). Since the protists, along with the archaea and bacteria, constitute the microbial ("microorganismal") community of the planet, this helps to substantiate the claim the microorganisms are the predominant and most diverse form of life on Earth. --Humans (Homo) are more closely related to yeast (Saccharomyces) than they are to corn (Zea). There are more genetic differences between E. coli and Bacillus than there are between humans and a paramecium. The protozoan

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Trichomonas is more closely related to the archaea than it is to the protozoan Trypoanosoma. When the tree branches are amplified there many other similar surprises to biologists. --Most biology and anthropology students have been presented with fossil and other structural evidence that humans (Homo) emerged a very short time ago on the evolutionary clock. The Tree confirms this evidence on the basis of comparative molecular genetic analysis.

Genomic Timescale of Procaryotic Evolution Comparison of protein sequences whose genes are common to the genomes of several procaryotes has resulted in a "genomic timescale of procaryotic evolution" and establishes the following dates for some major events in procaryotic evolution (Battistuzzi, et al. MC Evol Biol. 2004; 4: 44). The results are consistent with most other phylogenetic schemes that recognize higher-level groupings of procaryotes.

Table 1. Genomic timescale for some major events in procaryotic evolution

Origin of life: prior to 4.1 billion years ago (Ga) Origin of methanogenesis: 3.8 - 4.1 Ga Origin of phototrophy: prior to 3.2 Ga Divergence of the major groups of Archaea: 3.1 - 4.1 Ga Origin of anaerobic methanotrophy: after 3.1 Ga Colonization of land: 2.8 - 3.1 Ga Divergence of the major groups of Bacteria: 2.5 - 3.2 Ga Origin of aerobic methanotrophy: 2.5 - 2.8 Ga.

The time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Divergence times for the origin of anaerobic methanotrophy are compatible with carbon isotopic values found in rocks dated 2.8 - 2.6 Ga. The origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those structures (if biologically produced) would have been made by anoxygenic photosynthesizers. A well-supported group of three major lineages of Bacteria (Actinobacteria, Deinococcus, and Cyanobacteria), that have been called "Terrabacteria", are associated with an early colonization of land. Size and Distribution of Bacteria and Archaea Most procaryotic cells are very small compared to eukaryotic cells. A typical bacterial cell is about 1 micrometer in diameter while most eukaryotic cells are from 10 to 100 micrometers in diameter. Eukaryotic cells have a much greater volume of cytoplasm and a much lower surface : volume ratio than procaryotic cells. A typical procaryotic cell is about the size of a eukaryotic mitochondrion. Since procaryotes are too small to be seen except with the aid of a microscope, it is usually not appreciated that they are the most abundant form of life on the planet, both in terms of biomass and total numbers 8

of species. For example, in the sea, procaryotes make up 90 percent of the total combined weight of all organisms. In a single gram of fertile agricultural soil there may be in excess of 109 bacterial cells, outnumbering all eukaryotic cells there by 10,000 : 1. About 3,000 distinct species of bacteria and archea are recognized, but this number is probably less than one percent of all the species in nature. These unknown procaryotes, far in excess of undiscovered or unstudied plants, are a tremendous reserve of genetic material and genetic information in nature that awaits exploitation. Procaryotes are found in all of the habitats where eukaryotes live, but, as well, in many natural environments considered too extreme or inhospitable for eukaryotic cells. Thus, the outer limits of life on Earth (hottest, coldest, driest, etc.) are usually defined by the existence of procaryotes. Where eukaryotes and procaryotes live together, there may be mutualistic associations between the organisms that allow both to survive or flourish. The organelles of eukaryotes (mitochondria and chloroplasts) are thought to be remnants of Bacteria that invaded, or were captured by, primitive eukaryotes in the evolutionary past. Numerous types of eukaryotic cells that exist today are inhabitated by endosymbiotic procaryotes. From a metabolic standpoint, the procaryotes are extraordinarily diverse, and they exhibit several types of metabolism that are rarely or never seen in eukaryotes. For example, the biological processes of nitrogen fixation (conversion of atmospheric nitrogen gas to ammonia) and methanogenesis (production of methane) are metabolically-unique to procaryotes and have an enormous impact on the nitrogen and carbon cycles in nature. Unique mechanisms for energy production and photosynthesis are also seen among the Archea and Bacteria. The lives of plants and animals are dependent upon the activities of bacterial cells. Bacteria and archea enter into various types of symbiotic relationships with plants and animals that usually benefit both organisms, although a few bacteria are agents of disease. The metabolic activities of procaryotes in soil habitats have an enormous impact on soil fertility that can affect agricultural practices and crop yields. In the global environment, procaryotes are absolutely essential to drive the cycles of elements that make up living systems, i.e., the carbon, oxygen, nitrogen and sulfur cycles. The origins of the plant cell chloroplast and plant-type (oxygenic) photosynthesis are found in procaryotes. Most of the earth's atmospheric oxygen may have been produced by free-living bacterial cells. The bacteria fix nitrogen and a substantial amount of CO2, as well. Bacteria or bacterial products (including their genes) can be used to increase crop yield or plant resistance to disease, or to cure or prevent plant disease. Bacterial products include antibiotics to fight infectious disease, as well as components for vaccines used to prevent infectious disease. Because of their simplicity and our relative understanding of their biological processes, the bacteria provide convenient laboratory models for study of the molecular biology, genetics, and physiology of all types of cells, including plant and animal cells.

STRUCTURE AND FUNCTION OF PROCARYOTIC CELLS Procaryotic cells have three architectural regions (Figure 4): appendages (proteins attached to the cell surface) in the form of flagella and pili; a cell envelope consisting of a capsule, cell wall and plasma membrane; and a cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions.

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Figure 4. Schematic drawing of a typical bacterium.

Surface Structures-Appendages Flagella are filamentous protein structures attached to the cell surface that provide swimming movement for most motile procaryotic cells. The flagellar filament is rotated by a motor apparatus in the plasma membrane allowing the cell to swim in fluid environments. Bacterial flagella are powered by proton motive force (chemiosmotic potential) established on the bacterial membrane, rather than ATP hydrolysis which powers eukaryotic flagella. Procaryotes are known to exhibit a variety of types of tactic behavior, i.e., the ability to move (swim) in response to environmental stimuli. For example, during chemotaxis a bacterium can sense the quality and quantity of certain chemicals in their environment and swim towards them (if they are useful nutrients) or away from them (if they are harmful substances).

Figure 5.Vibrio choleraehas a single polar flagellum for swimming movement. Electron Micrograph of Vibrio cholerae by Leodotia Pope, Department of Microbiology, University of Texas at Austin.

Fimbriae and...