The Main Themes of Microbiology Chapter 01 The Main Themes of Microbiology Lecture Outline See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes. Copyright © 2018 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education.

Chapter 1 Objectives List the various types of microorganisms. Identify multiple professions using microbiology. Describe the role and impact of microbes on the earth. Summarize the relative burden of human disease caused by microbes, emphasizing the differences between developed countries and developing countries. Differentiate among bacteria, archaea, and eukaryotic microorganisms. Make a time line of the development of microbiology from the 1600’s to today. List some recent microbiological discoveries of great impact. Explain what is important about the scientific method. Differentiate between the terms nomenclature, taxonomy, and classification. Create a mnemonic device for remembering taxonomic categories. Correctly write the binomial name for a microorganism. Draw a diagram of the three major domains. Describe the importance of the biogeochemical cycles and the role microbes play in maintaining the biogeochemical cylces.

General Biology Content for Chapter 1 Use the “General Biology Module” content and your textbook to review and master the general biology content found in chapter 1. Students should master the following content: The evolutionary timeline. The difference between prokaryotes and eukaryotes. The binomial nomenclature. Taxonomy and its levels of classification. Phylogeny (5 kingdoms vs. 3 domains). NOTE: Your professor will not be discussing this content in class. You will be expected to know this and you will be challenged to discuss this content in class and answer questions on it during in-class exercises, quizzes, and exams.

The Scope of Microbiology Microbiology: the specialized area of biology that deals with organisms too small to be seen with the naked eye Major groups of microorganisms: Bacteria Algae Protozoa Helminths Fungi Viruses: non-cellular (acellular), parasitic, protein-coated genetic elements that cause harm to host cells

The Scope of Microbiology Microbes are easy and difficult to study Reproduce rapidly, large populations can be grown in the laboratory Can’t be seen directly, must be analyzed through indirect methods in addition to using microscopes Microbiologists study: Cell structure and function Growth and physiology Genetics Taxonomy and evolutionary history Interactions with living and nonliving environment

Branches of Microbiology Medical Microbiology Deals with microbes that cause diseases in humans and animals Public Health Microbiology and Epidemiology Monitor and control the spread of diseases in communities USPHS, CDC, WHO

Branches of Microbiology Immunology Complex web of protective substances and cells produced in response to infection Includes vaccination, blood testing, and allergy Role of the immune system in cancer and autoimmune diseases Industrial Microbiology Safeguards our food and water Biotechnology Microbes used to create amino acids, beer, drugs, enzymes, and vitamins

Branches of Microbiology Agricultural Microbiology Relationships between microbes and domesticated plants and animals Plant specialists, animal specialists Environmental Microbiology Study the effect of microbes on the earth’s diverse habitats Aquatic, soil, and geomicrobiology, and astrobiology

The Impact of Microbes on Earth Bacteria are ubiquitous. They are found: deep in the earth’s crust polar ice caps oceans inside the bodies of plants and animals

Microbial Involvement in Shaping Our Planet Microbes are deeply involved in the flow of energy and food through the earth’s ecosystems Bacteria: anoxygenic photosynthesis The production of oxygen by microbes allowed species diversification Photosynthetic microorganisms (bacteria and algae) account for more than 70% of the earth’s photosynthesis, contributing the majority of the oxygen to the atmosphere Examples of Microbial Habitats: Pond with Algae

Microbial Involvement in Shaping Our Planet Decomposition: Breakdown of dead matter and wastes Accomplished by bacteria and fungi Microbes are the main forces that drive the structure and content of soil, water, and atmosphere Gas production by microbes Microbes living within the earth’s crust Bacteria and fungi living in complex associations with plants and animals (b) © Michel & Christine Denis-Huot/Science Source

Concept Check What types of organisms are considered microbes? What types of cells can viruses infect? List and describe three branches of microbiology.

Special Topic: The Natural Recycling of Bio-elements (Chapter 24) Biogeochemical cycles: All elements ultimately originate from a nonliving, long-term reservoir in the atmosphere, lithosphere, or the hydrosphere Elements cycle between the abiotic environment and the biotic environment Recycling maintains a necessary balance of nutrients in the biosphere so that they do not build up or become unavailable

Special Topic: The Natural Recycling of Bio-elements (Chapter 24) Biogeochemical cycles (cont’d): Cycles are complex systems that rely on the interplay of primary producers, consumers, and decomposers All organisms participate in the recycling, but only certain categories of microorganisms have the metabolic pathways for converting inorganic compounds from one nutritional form to another

Special Topic: The Natural Recycling of Bio-elements (Chapter 24) Biogeochemical cycles (cont’d): Atmospheric Cycles: Carbon Cycle Nitrogen Cycle Sedimentary Cycles: Sulfur Cycle Phosphorous Cycle

The Carbon Cycle (Chapter 24)

The Nitrogen Cycle (Chapter 24) Symbiotic relationship between rhizobia and legumes: Rhizobia: bacteria Infect legume roots and produce root nodules Enzyme system of rhizobia supplies a constant source of reduced nitrogen to the plant Nitrification: Nitrosomonas, Nitrosospira, and Nitrosococcus oxidize NH3 to NO2- Nitrobacter, Nitrosospira, and Nitrococcus perform the final oxidation of NO2- to NO3- Denitrification: Conversion of nitrate to atmospheric nitrogen Bacteria: Bacillus, Pseudomonas, Spirillum, Thiobacillus NO3-  NO2-  NO  N2O  N2 (gas) Denitrification Ammonification: decomposition of organic matter by Clostridium and Proteus produces NH4+

Sulfur Cycle (Chapter 24) Sedimentary Deposits: Rocks, Oceans, Lakes, Swamps Sources Certain Bacteria: Convert one form of sulfur to another Thiobacilli use sulfur, sulfate, thiosulfate and release acid in the process. The acid produced by Thiobacilli living on rocks help release the phosphorous from the rocks to help start the phosphorous cycle. Sulfur, Hydrogen Sulfide, Sulfate, Thiosulfate Animals: Only use an organic source of sulfur (amino acid cysteine or methionine). Plants and certain bacteria: Use only the sulfate

The Phosphorous Cycle Thiobacilli-Releases sulfuric acid on rocks releasing the inorganic phosphate

Other Cycles (Chapter 24) Involvement of microbes in cycling elements and compounds is escalated by the introduction of toxic substances in the environment. Some are converted into less harmful substances by microbial actions Bioaccumulation: Some persist and flow along with nutrients into all levels of the biosphere

Concept Check Which organisms participate in the biogeochemical cycles?   Of the two main types of biogeochemical cycles, which one does the sulfur cycle fall under? Of the two main types of biogeochemical cycles, which one does the carbon cycle fall under? Why is recycling important?

Concept Check Cycles are complex and require the interplay between producers, consumers, and decomposers. What would be the consequence of removing the decomposers from this complex interplay?   Name the two different types of environments involved in the biogeochemical cycles. Which organisms are the main decomposers? How is the carbon fixed by the producers involved in the carbon cycle?

Concept Check How is the carbon recycled back into the environment by the consumers or decomposers?   What is in the legume nodules that help in nitrogen fixation? How is the nitrogen recycled back into the environment? True or False: Bacteria plays a role in each step of the nitrogen cycle.

In-Class Exercise What is the only form of sulfur that animals can use? Which bacteria causes the breaking down of rocks as it converts sulfur from one form to the other? Describe one consequence that may result if the inorganic phosphate was not supplied to consumers.

Human Use of Microorganisms (also part of Chapter 25) Humans have been using microorganisms for thousands of years to improve life and even shape civilizations Yeast for production of bread, wine, and beer Other fungi used for cheese production Moldy bread used in Egypt to treat wounds

Human Use of Microorganisms (also part of Chapter 25) Biotechnology: Manipulation of microorganisms to make products in an industrial setting Genetic Engineering: Manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms (GMOs) (a) NREL/US Department of Energy/Dennis Schroeder (b) © Bloomberg via Getty Images

Human Use of Microorganisms (also part of Chapter 25) Recombinant DNA technology: Techniques that allow the transfer of genetic material from one organism to another and deliberately alter DNA Bioremediation: Introduction of microbes into the environment to restore stability or to clean up toxic pollutants (c) © Accent Alaska.com/Alamy

Concept Check True/False: Microscopic organisms produce more oxygen than plants. Name three products produced by genetically modified organisms that benefit humans. Describe one method in which microbes are used for bioremediation. True/False: All microbes cause disease.

Infectious Diseases and the Human Condition Pathogen: any agent such as a virus, bacterium, fungus, protozoan, or helminth that causes disease Nearly 2000 different microbes can cause disease

Infectious Diseases and the Human Condition Malaria: Kills between 440,000 and 700,000 people every year Transmitted by mosquitoes Prevention of infection is through the use of bed nets, which although inexpensive, are too expensive for poor families New (emerging) diseases as well as older (reemerging) diseases are increasing Ebola, AIDS, hepatitis C, and viral encephalitis Polio, leprosy, and parasitic worm diseases have largely been eradicated Certain diseases once considered noninfectious are now found to be caused by microbes: Gastric ulcers caused by Helicobacter pylori Link between certain cancers and bacteria and viruses Cocksackie virus has been associated with diabetes and schizophrenia Multiple sclerosis, OCD, coronary artery disease, obesity linked to chronic microbial infections

Infectious Diseases and the Human Condition First Golden Age of Microbiology: “obvious” diseases were characterized and cures or preventions were devised Today, we are discovering the subtler side of microorganisms and the quiet, slow, destructive diseases they cause Female infertility caused by Chlamydia infection Liver cancer (hepatitis viruses) and cervical cancer (human papillomavirus) An increasing number of patients with weakened immune systems are subject to infections by common microbes not pathologic to healthy people Drug-resistant microbes also contribute to the increase in infectious disease

General Characteristics of Microorganisms Bacterial and Archaeal cells: About 10x smaller than eukaryotic cells Lack organelles: small, double-membrane-bound structures that perform specific functions The majority of microorganisms are single-celled (all bacterial and archaeal and some eukaryotes)

General Characteristics of Microorganisms Helminths (worms) are not microorganisms but are included in the study of infectious disease: They are transmitted similarly to bacterial diseases The human body responds to them in the same way as it responds to bacterial diseases Five Types of Microorganisms

Lifestyles of Microorganisms Majority of microorganisms: Live in habitats such as soil and water Are relatively harmless and often beneficial Derive food and other factors from the nonliving environment Parasites: Harbored and nourished by the host Cause damage and disease in the host

Concept Check Why is there a difference between the top 10 causes of death in the U.S. versus worldwide? Name three connections between diseases considered to be noninfectious and a microbe. In terms of size, how are eukaryotes different from bacteria and archaea? Give three examples of eukaryotic organelles. Why are helminths (worms) considered in the study of microbiology?

The Historical Foundations of Microbiology Early Ideas About Disease Transmission Certain foods spoiled, became inedible, or caused illness Black plague and smallpox caused by some kind of transmissible matter Belief in spontaneous generation-Disproved by Louis Pasteur

Development of the Microscope Robert Hooke: First observations of microbes in the 1600s Antonie van Leeuwenhoek: Made a crude microscope to examine threads in fabrics Made drawings of what he called “animalcules” in rainwater and scraped from his teeth (a) © Biophoto Associates/Science Source; (b) CDC/Dr. Lucille K. Georg © Tetra Images/Alamy RF

The Century of Biology 1970s: Discovery of restriction enzymes 1980s: The invention of the PCR technique 2000s: The importance of small RNAs 2010s: The role of the human microbiome Science is an ever-evolving collection of new information

The Development of Medical Microbiology Early experiments showed that microbes are everywhere: Air and dust are full of them The entire surface of the earth and its waters, and all objects are inhabited by them

The Discovery of Spores and Sterilization John Tyndall: Found that microbes in the dust and air have high heat resistance Ferdinand Cohn: Discovered and described bacterial endospores Sterile: completely free of all life forms including endospores and virus particles

Development of Aseptic Techniques Robert Koch: Linked a specific microorganism with a specific disease Dr. Oliver Wendell Holmes and Dr. Ignaz Semmelweis: Showed that women became infected in the maternity ward after examinations by physicians who had been working in the autopsy rooms

Development of Aseptic Techniques Joseph Lister: First to utilize hand washing and misting operating rooms with antiseptic chemicals Techniques became the foundation for modern microbial control still in use today © Bettmann/Corbis

Discovery of Pathogens and the Germ Theory of Disease Pasteur: Invented pasteurization Showed that human diseases could arise from infection Robert Koch: Established a series of proofs that verified the germ theory of disease

Human Disease Connection: Bacterium Pneumococcal Pneumonia (Respiratory Disease) Etiology (causative agent) Prevention Vaccination Streptococcus pneumonia (in 40% of cases) Culture/Diagnosis Mode of Transmission Epidemiology Symptoms; Physical Exam; Lab Tests Virulence Factors Symptoms Treatment Droplet Contact (Inhalation) Children Under 2 and Adults Above 65 Capsule; Hemolysins Fever, Cough, Shortness of Breath, Rapid Breathing, Chest Pain Broad-Spectrum Antibiotic

Human Disease Connection: Fungus (Gastrointestinal Disease) Oral Candidiasis (Gastrointestinal Disease) Etiology (causative agent) Prevention Good Oral Hygiene Candida albicans Culture/Diagnosis Mode of Transmission Epidemiology Virulence Factors Easily Detectable by Examination, Gram-Staining Symptoms Treatment Commonly Found in Humans, but Becomes Opportunistic. Occurs More Often in Immuno-compromised Individuals Adhesins Redness, Difficulty Swallowing; Angular Cheilitis (cracks corner of mouth) Antifungals

Human Disease Connection: Protozoan (Neurological Disease) Toxoplasmosis (Neurological Disease) Properly Preparing and Cooking Food (Care Cleaning Cat Litter Box) Etiology (causative agent) Prevention Toxoplasma gondii Culture/Diagnosis Mode of Transmission Epidemiology Virulence Factors Blood or Amniotic Fluid Test Symptoms Treatment Oral Route Rates Differ by Country; Concern in Pregnant Women Toxins Mostly None in Adults; Mild-flu; Birth Defects Anti-parasitic

Human Disease Connection: Virus (Reproductive Tract Disease) Genital Herpes (Reproductive Tract Disease) Etiology (causative agent) Prevention Avoidance Culture/Diagnosis Herpes Simplex Virus 1 and 2 Mode of Transmission Clinical Presentation and PCR Epidemiology Virulence Factors Symptoms Treatment Direct Contact 536 Million Infected Internationally Latency Genital Lesions Anti-virals

Human Disease Connection: Helminth River Blindness (Eye and Skin Disease) Etiology (causative agent) Prevention Avoid Black Fly Onchocerca volvulus Culture/Diagnosis Mode of Transmission Worms Visible in Eye; Histology of Skin Snip Epidemiology Virulence Factors Symptoms Treatment Black Fly Bite 18-40 million worldwide Fly Larvae: Evasion of Immune Response Skin Nodules; Blindness Anti-parasitic

Human Disease Connection: Alga (Integumentary Disease) Protothecosis (Integumentary Disease) Prevention Etiology (causative agent) Immune-competence Culture/Diagnosis Prototheca wickerhami Mode of Transmission Epidemiology Virulence Factors Examination of Tissue Symptoms Treatment Direct Contact Contact with Contaminated Soil and Water Toxins Skin Ulcers Antifungals

Concept Check Spontaneous generation was disproven by _______________. Polymerase chain reaction is used to copy ________________. The Aseptic technique ensures _________________________.

Concept Check 1. Which of the following is not considered a microorganism? A. Mosquito B. Protozoa C. Bacteria D. Viruses E. Fungi 2. The microorganisms that do not have a nucleus in their cells are called ________________. A. Decomposers B. Prokaryotes C. Pathogens D. Eukaryotes E. Fermenters 3. Which of the following is not a human use of microorganisms? A. Baking bread B. Treating water and sewage C. Breaking down chocolate D. Mass producing antibiotics E. Cleaning up oil spills

Concept Check 4. Disease-causing microorganisms are called ____________. A. Decomposers B. Prokaryotes C. Pathogens D. Eukaryotes E. Fermenters 5. Which of the following is a unique characteristic of viruses that distinguishes them from the other major groups of microorganisms? A. Cause human disease B. Lack a nucleus C. Cannot be seen without a microscope D. Contain genetic material E. Lack cell structure 6. Sterile refers to A. Pathogen free B. Absence of spores C. Absence of any life forms and spores and viral particles D. Pasteurized E. Homogenized