Ch. 1 The Main Themes of Microbiology PDF

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1.1 The Scope of Microbiology Microbes in the word are ubiquitous meaning they can survive in all natural habitats and in most human created habitats. They exist in the ocean to a depth of 7 miles, in hot springs and thermal vents, in toxic waste dumps and in clouds. They are measured in micrometers (um), nanometers (nm), and millimeters (mm). Whereas macroorganisms are measured in centimeters (cm). Golden Age of Microbiology: 1850-1950 Louis Pasteur and others invented the science of microbiology. Today with the help of molecular biology we can describe this as a Second Golden Age. Microbiology is a science that studies tiny life that is not readily observed without magnification. It studies the genetic, the physiology and the characteristics of microbes that may be harmful or beneficial. It studies the ways they interact with the environment and organisms and the ways they can be used in agriculture. Microscopic organisms are called microorganisms or microbes. The major groups of microorganisms are: Bacteria Viruses Fungi Protozoa Algae Helminths (parasitic worms) Branches in Microbiology: Bacteriology Mycology Protozoology Virology Phycology or Algology Morphology Physiology Taxonomy Microbial Genetics Molecular Biology Microbial Ecology

Microbiologist specialties branches: Geomicrobiologists: Microbes on the development of earth’s crust. Marine Microbiologists: Microbes in oceans and waters. Medical Technologists: Test pathogenic microbes and diseases associated with them. Nurse Epidemiologist: Analyze occurrence of infectious diseases in hospitals Astrobiologists: Possibility of organisms in space.

Occupations in Microbiology: Public Health Microbiology and epidemiology - USPHS/ CDC organizations. Mort weekly report. Biotechnology and Industrial Microbiology - Beer, vaccines, vitamins, drugs, enzymes, etc Environmental Microbiology - Ecological relationships Immunology - Protective substances or reactions activated by invading microbes Genetic Engineering and Recombinant DNA Tech - Alterations of DNA to create plants/animals Agricultural Microbiology - Plant disease, soil fertility, domesticated animals. Food Microbiologists - Food spoilage, food borne diseases and production of food.

Biotechnology: The manipulation of microorganisms to make products in an industrial setting. Genetic engineering:

1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environment. Prokaryotic Cells: Early microorganisms that dominated earth’s life for 3.5 billion years. Simple structured cells that lacked a nucleus. All prokaryotes are single celled microorganisms. They cannot form other organisms by clustering together. They include bacteria and archaea. Karyon = Meaning nucleus. Organelles: Internal structures of a cell. Eukaryotic Cells: More complex cells that developed from the prokaryotic cells in a process called endosymbiosis, with a nucleus included and many other organelles. They appeared 2 billion years ago, 1.5 billion years after the appearance of Prokaryotic

cells. Early eukaryotic cells gave rise to fungi, plants, worms and insects about 1 billion year after the first appearance of Eukaryotic cells. Only some of the eukaryotic cells form microorganisms, especially algae, protozoa, molds and yeast, worms and arthropods. They can be either single celled or multicellular microorganisms. Photosynthesis: Light-fueled conversion of carbon dioxide to organic material and oxygen. Microorganisms were responsible for the change of the atmosphere from no oxygen to oxygen. Today they are still responsible for 50% of earth's photosynthesis contributing to the majority of oxygen to the atmosphere. Decomposition: Nutrient recycling. Breakdown of dead matter into simple compounds. Earth’s temperature: Greenhouse of gases. Carbon dioxide, methane create insulation to the atmosphere and help retain heat. Based on weight 50 % of all organisms exist within and and beneath the earth’s crust. Protection: Some microbes protect against disease and assist with nutrient absorption. Bacteria: Mycobacterium tuberculosis (rod-shaped cell): Cause of tuberculosis Fungi: Histoplasma capsulatum (lolipop-like reproductive structure): Cause of the Ohio River Fever Algae: Spirogyra filament Desmids Virus: Herpes simplex: Cause of cold sores Protozoa: Oxytricha trifallax (bearing cillia) Helminths: Trichinella spiralis (roundworms): Causes trichinellosis

Arthropods: Carriers of infectious diseases. Ex: fleas and ticks.

1.3 Human Use of Microbes Yeast is a type of microscopic fungi which causes bread to rise and ferment sugar to make alcoholic beverages. Moldy bread gave origin to Aspirin. Biotechnology is the manipulation of microorganisms to make products in an industrial setting. Genetic engineering is a newer area of biotechnology that manipulates the genetics of microbes, plants, and animals for the purpose of creating new products. Recombinant DNA: The technology used to switch genetic material from one organism to another. Bacteria and fungi were some of the first organisms. Microbes can be engineered to synthesize desirable proteins such as drugs, hormones and enzymes.

1.4 Microbial roles in infectious diseases Parasitism: Non free living style. Parasites live in or on the body of a larger organism called the host. NTD’s: Common neglected diseases. Neglected Tropical Diseases: Ascariasis Hookworm infection Onchocerciasis (river blindness) Lymphatic filariasis Schistosomiasis Trachoma Trichuriasis Emerging and Reemerging Diseases: Older well known diseases that increase in occurrence. Ex: TB, influenza, malaria, cholera and hepatitis B. Zoonoses: Infectious diseases native to animals that can be transmitted to humans.

1.5 The Historical Foundations of Microbiology Spontaneous generation: The era when people believed that certain types of living things gave birth from decomposing matter or nonliving things.

Abiogenesis the idea of some type of living things arose from decomposing matter or non living things. Embraced the spontaneous generation. Biogenesis: The idea that living things can arise only from other living things of the same kind. Francesco Redi: The fist to test the spontaneous generation theory in Italy encouraging the biogenesis idea. Louis Pasteur: In the mid 1800’s studied the role of microorganisms in the fermentation of beer and wine. Developed the vaccine for rabies and anthrax. Invented pasteurization. Pasteurization: The process of using heat, usually under 100C to eliminate pathogens. Antoine Van Leeuwenhoek: Designed the single-lens microscope hand fashioned. Deductive Reasoning Approach: Used in the scientific method. The use of a general observation of some type to develop a set of facts to explain the phenomenon. Hypothesis: The early explanation of a phenomenon. A valid hypothesis needs to allow for experimentation and testing. Inductive Reasoning: Use of the scientific method. The application of specific observations to develop a general explanation. Often used in early phases of evaluation. Can formulate a generalization to be tested deductively. Theory: The last stage of a scientific method. The last level of approval of an hypothesis after supporting proof of multiple testing. Law: A theory that is so accurate and predictable that generates a high level of trust. Edward Jenner’s monumental discovery: Called the father of immunology. The first to use the scientific method to test the concept of safely conferring artificial immunity long before there was an understanding of an immune system through rigorous experimentation and inoculation of people against diseases. He experimented on cowpox from cows and smallpox from humans. He called his technique a vaccination from the Latin Vaca. Ferdinand Cohn: Discovered heat-resistant bacterial endospores.

Sterile: Meaning completely free of all infectious agents. Robert Koch: Linked diseases to microorganisms. Joseph Lister: English surgeon that introduced the aseptic techniques into the hospitals. It involved disinfecting the hands and the air with strong antiseptic chemicals such as phenol prior to surgery. Also the application of heat sterilization. Germ theory of disease: The theory that some diseases emerge from microorganisms.

1.6 Taxonomy: Organizing, Classifying and Naming Microorganisms, Identify. Taxonomy: The formal system to be followed for organizing, classifying and naming things. Invented by Carl Von Linne. Viruses are not included in any type of classification or evolutionary schemes because they are not cells. They have a special taxonomy. Classification: Orderly arrangement of organisms into groups that indicate evolutionary relationships and history. Microbial Nomenclature is the microbes language. The names used to describe and recognize microbes. Assigning names to microbes. Originated from the Greek or Latin language. The ends of each name are always revised to have a latin ending if otherwise. Identification: Determine its exact identity and placement in taxonomy. Levels of Classification: Arranged into several ranks called hierarchy. Hierarchy of taxonomy: Is the classification of microbes. Levels of Hierarchy: 1. 2. 3. 4. 5.

Domain Kingdom Phylum or division Class Order

6. Family 7. Genus 8. Species Prefixes for hierarchy: “Super-” meaning above. “Sub-” meaning below. Eukarya: Domain where humans belong. Animalia: Kingdom where humans belong. Chordata: Phylum where humans belong. Mammalia: Class where humans belong. Primates: Order where humans belong. Hominoidea: Family where humans belong. Homo: Genus where humans belong. Sapiens: Species where humans belong. Five-kingdom System: 1. Monera 2. Fungi 3. Protists 4. Plants 5. Animals

Three most broad Domains: 1. Bacteria: Of prokaryotic cells. Contain the kingdom on Monera. 2. Eukarya: Of eukaryotic cells. Contain the kingdoms of fungi, protists, plants, animals. 3. Archaea: Of eukaryotic cells that live in extreme environments. Scientific name: Also known as specific epithet. Is assigned using a binomial system of nomenclature. A combination of the genus name followed by the species name. The Genus first letter is capitalized and the species name start with lowercase. It should be italicized or underlined.

1.7 The Origin and Evolution of Microorganisms

Phylogeny: The natural relationship between groups of living things. Evolution: Living things change gradually through billions of years. The process of evolution is selective. It is founded in two premises. (1) That all new species originate from preexisting species through inheritance of traits, and (2) that closely related organisms have similar features because they evolve from common ancestral forms. Morphology: The structure. Physiology: The function. Genetics: The inheritance. Robert Whitthaker: Developed a five-kingdom system....