1. The Main Themes of Microbiology
Chapter 01
The Main Themes of Microbiology
Lecture Outline
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2. 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.

3. 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.

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

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

13. 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

14. 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

15. 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

16. The Carbon Cycle (Chapter 24)

17. 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+

18. 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

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

20. 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

21. 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?

22. 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?

23. 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.

24. 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.

25. 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

26. 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

27. 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

28. 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.

29. 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

30. 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

31. 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

32. 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)

33. 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

34. 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

35. 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?

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

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

51. 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

52. 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