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. Section 1.1: 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

4. 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

5. 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

6. 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

7. 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

8. Section 1.2: The Impact of Microbes on Earth
Evolutionary Time Line
Microbes have shaped the development of the earth’s habitats and the evolution of other life forms for billions of years
Single-celled organisms arose 3.5 billion years ago and were the only living inhabitants until ~2.9 billion years ago
Bacteria, archaea, and eukaryotes arose from the last universal common ancestor (LUCA)

9. The Impact of Microbes on Earth
Eukary: true-nucleus
Cells with a nucleus are classified as eukaryotes
Prokary: pre-nucleus
Bacteria and archaea do not have a nucleus and have been traditionally classified as prokaryotes
This classification is no longer used because bacteria and archaea are so distant genetically

10. 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

11. 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

12. 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

13. Special Topic: The Natural Recycling of Bioelements (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 Bioelements (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 Bioelements (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, Nitrospira, and Nitrosococcus oxidize NH3 to NO2-
Nitrobacter, Nitrosospira, and Nitrosococcus 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. Section 1.3: 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

22. 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

23. 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

24. Section 1.4: 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

25. 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

26. Infectious Diseases and the Human Condition
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
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

27. 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

28. Section 1.5: 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)

29. 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

30. 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

31. Section 1.6: 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. Nomenclature: Assigning Specific Names
Section 1.7: Naming, Classifying, and Identifying Microorganisms
Nomenclature: Assigning Specific Names
Nomenclature:
The assignment of scientific names to the various taxonomic categories and individual organisms
Understanding and appreciation of microorganisms will be improved by learning a few general rules about how they are named

40. Binomial System of Nomenclature
A combination of the generic (genus) and species name
The genus name is always capitalized and the species name begins with a lower case letter
Both names should be italicized when in print or underlined when written by hand
Abbreviations:
The genus name can be abbreviated to save space or if the genus name has already been stated
Example: Staphylococcus aureus can be abbreviated as S. aureus

41. Classification: Constructing Taxonomy
Attempts the orderly arrangement of organisms into a hierarchy of taxa (categories)
Levels of Classification
From most general to most specific:
Domain
Kingdom
Phylum or Division
Class
Order
Family
Genus
Species
Identification:
The process of discovering and recording the traits of organisms so they can be recognized or named and placed in a taxonomic scheme

42. Origin and Evolution of Microorganisms
Taxonomy:
The science of classifying biological species
Developed by Carl von Linné in the 1700s
Lays down the basic rules for classification
Establishes taxonomic categories
Used to organize all of the forms of modern and extinct life

43. Origin and Evolution of Microorganisms
Phylogeny:
The taxonomic scheme that represents the natural relatedness between groups of living things
Based on evolution

44. Universal Tree of Life Charles Darwin and Ernst Haeckel:
Two kingdoms: Plants and Animals
Based on morphological characteristics
Third and fourth kingdoms named by Haeckel: Protista and Monera
Robert Whittaker
Added a fifth kingdom: Fungi
All kingdoms encompassed the two cell types: prokaryotic and eukaryotic
Whittaker system became the standard

45. Tree of Life: A phylogenetic System
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