1. Microorganisms and Microbiology
Chapter 1
Microorganisms and Microbiology

2. I. Introduction to Microbiology
1.1 The Science of Microbiology
1.2 Microbial Cells
1.3 Microorganisms and Their Environments
1.4 Evolution and the Extent of Microbial Life
1.5 The Impact of Microorganisms on Humans
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3. 1.1 The Science of Microbiology
Microbiology revolves around two themes:
1. Understanding basic life processes
Microbes are excellent models for understanding cellular processes in unicellular and multicellular organisms
2. Applying that knowledge to the benefit of humans
Microbes play important roles in medicine, agriculture, and industry
Because microorganisms are central to the very functioning of the biosphere, the science of microbiology is the foundation of all the biological sciences.
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4. 1.1 The Science of Microbiology
The Importance of Microorganisms
Oldest form of life
Largest mass of living material on Earth
Carry out major processes for biogeochemical cycles
Can live in places unsuitable for other organisms
Other life forms require microbes to survive
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5. 1.2 Microbial Cells The Cell
A dynamic entity that forms the fundamental unit of life (Figure 1.2)
Cytoplasmic (cell) membrane
Barrier that separates the inside of the cell from the outside environment
Cell wall
Present in most microbes, confers structural strength
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6. Flagella Nucleoid Membrane Wall Figure 1.2
Figure 1.2 Bacterial cells and some cell structures.
Nucleoid
Membrane
Wall
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7. 1.2 Microbial Cells Characteristics of Living Systems (Figure 1.3)
Metabolism: chemical transformation of nutrients
Reproduction: generation of two cells from one
Differentiation: synthesis of new substances or structures that modify the cell (only in some microbes)
Communication: generation of, and response to, chemical signals (only in some microbes)
Movement: via self-propulsion, many forms in microbes
Evolution: genetic changes in cells that are transferred to offspring
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8. I. Properties of all cells
Figure 1.3 (Part 1 of 2)
I. Properties of all cells
Compartmentalization and metabolism A cell is a compartment that takes up nutrients from the environment, transforms them, and releases wastes into the environment. The cell is thus an open system.
Growth Chemicals from the environment are turned into new cells under the genetic direction of preexisting cells.
Evolution Cells contain genes and evolve to display new biological properties. Phylogenetic trees show the evolutionary relationships between cells.
Distinct species
Ancestral cell
Cell
Environment
Distinct species
Figure 1.3 The properties of cellular life.
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9. II. Properties of some cells
Figure 1.3 (Part 2 of 2)
II. Properties of some cells
Motility Some cells are capable of self-propulsion.
Differentiation Some cells can form new cell structures such as a spore, usually as part of a cellular life cycle.
Communication Many cells communicate or interact by means of chemicals that are released or taken up.
Spore
Figure 1.3 The properties of cellular life.
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10. 1.2 Microbial Cells Cells as Catalysts and as Coding Devices
1. Cells carry out chemical reactions
Enzymes: protein catalysts of the cell that accelerate chemical reactions (Figure 1.4)
2. Cells store and process information that is eventually passed on to offspring during reproduction through DNA (deoxyribonucleic acid) and evolution (Figure 1.4)
Transcription: DNA produces RNA
Translation: RNA makes protein
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11. Genetic functions Catalytic functions ATP
Figure 1.4
Genetic functions
Catalytic functions
DNA
Energy conservation: ADP  Pi
ATP
Metabolism: generation of precursors of macro- molecules (sugars, amino acids, fatty acids, etc.)
Replication
Transcription
RNA
Enzymes: metabolic catalysts
Translation
Proteins
Figure 1.4 The catalytic and genetic functions of the cell.
Growth
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12. 1.2 Microbial Cells Growth
The link between cells as machines and cells as coding devices
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13. 1.3 Microorganisms and Their Environments
Microorganisms exist in nature in populations of interacting assemblages called microbial communities (Figure 1.5)
The environment in which a microbial population lives is its habitat
Ecosystem refers to all living organisms plus physical and chemical constituents of their environment
Microbial ecology is the study of microbes in their natural environment
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14. Figure 1.5 Figure 1.5 Microbial communities.
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15. 1.3 Microorganisms and Their Environments
Diversity and abundances of microbes are controlled by resources (nutrients) and environmental conditions (e.g., temp, pH, O2)
The activities of microbial communities can affect the chemical and physical properties of their habitats
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16. 1.3 Microorganisms and Their Environments
Microbes also interact with their physical and chemical environment
Ecosystems greatly influenced (if not controlled) by microbial activities
Microorganisms change the chemical and physical properties of their habitats through their activities
For example, removal of nutrients from the environment and the excretion of waste products
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17. 1.4 Evolution and the Extent of Microbial Life
The First Cells
First self-replicating entities may not have been cells
Last universal common ancestor (LUCA): common ancestral cell from which all cells descended
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18. 1.4 Evolution and the Extent of Microbial Life
Life on Earth through the Ages (Figure 1.6)
Earth is 4.6 billion years old
First cells appeared between 3.8 and 3.9 billion years ago
The atmosphere was anoxic until ~2 billion years ago
Metabolisms were exclusively anaerobic until evolution of oxygen-producing phototrophs
Life was exclusively microbial until ~1 billion years ago
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19. Figure 1.6 Origin of Earth (4.6 bya)
Mammals
Humans
Vascular plants
Shelly invertebrates
Origin of Earth (4.6 bya)
Present
 20% O2
1 bya
4 bya
Origin of cellular life O2
Mic
rob
ial
life
for ms
only
3 bya
2 bya
Anoxygenic phototrophic bacteria
Algal diversity
Anoxic Earth
Earth is slowly oxygenated
Modern eukaryotes
Origin of cyanobacteria
Figure 1.6 A summary of life on Earth through time and origin of the cellular domains.
Bacteria
LUCA
Archaea
Eukarya 4 3 2 1
bya
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20. 1.4 Evolution and the Extent of Microbial Life
Microbes found in almost every environment imaginable
Global estimate of 5  1030 cells
Most microbial cells are found in oceanic and terrestrial subsurfaces
Microbial biomass is significant and cells are key reservoirs of essential nutrients (e.g., C, P, N)
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21. 1.5 The Impact of Microorganisms on Humans
Microorganisms can be both beneficial and harmful to humans
Emphasis typically on harmful microorganisms (infectious disease agents, or pathogens)
Many more microorganisms are beneficial than are harmful
Microorganisms as disease agents
Control of infectious disease during last century (Figure 1.8)
Nitrogen fixing bacteria: For example, legumes, which live in close association with bacteria that form structures called nodules on their roots, convert atmospheric nitrogen into fixed nitrogen that the plants use for growth. The activities of the bacteria reduce the need for costly and polluting plant fertilizer.
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22. Figure 1.8
1900
Today
Influenza and pneumonia
Heart disease
Tuberculosis
Cancer
Gastroenteritis
Stroke
Heart disease
Pulmonary disease
Stroke
Accidents
Kidney disease
Diabetes
Accidents
Alzheimer’s disease
Cancer
Influenza and pneumonia
Infant diseases
Kidney disease
Septicemia
Infectious disease
Diphtheria
Figure 1.8 Death rates for the leading causes of death in the United States: 1900 and today.
Nonmicrobial disease
Suicide
100
200
100
200
Deaths per 100,000 population
Deaths per 100,000 population
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23. 1.5 The Impact of Microorganisms on Humans
Microorganisms and Agriculture
Many aspects of agriculture depend on microbial activities (Figure 1.9)
Positive impacts
nitrogen-fixing bacteria
cellulose-degrading microbes in the rumen
regeneration of nutrients in soil and water
Negative impacts
diseases in plants and animals
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24. Fatty acids (Nutrition for animal) CO2  CH4 (Waste products)
Figure 1.9
N2  8H
2NH3  H2
Soybean plant
N-cycle
S-cycle
Rumen
Figure 1.9 Microorganisms in modern agriculture.
Grass
Cellulose
Glucose
Microbial fermentation
Fatty acids (Nutrition for animal)
CO2  CH4 (Waste products)
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25. 1.5 The Impact of Microorganisms on Humans
Microorganisms and Food
Negative impacts
Food spoilage by microorganisms requires specialized preservation of many foods
Positive impacts
Microbial transformations (typically fermentations) yield
dairy products (e.g., cheeses, yogurt, buttermilk)
other food products (e.g., sauerkraut, pickles, leavened breads, beer)
Microorganisms also play important roles in the food industry, both harmful and beneficial. Because food fit for human consumption can support the growth of many microorganisms, it must be properly prepared and monitored to avoid transmission of disease.
Foods that benefit from the effects of microorganisms include cheese, yogurt, buttermilk, sauerkraut, pickles, sausages, baked goods, and alcoholic beverages.
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26. 1.5 The Impact of Microorganisms on Humans
Microorganisms, Energy, and the Environment (Figure 1.11)
The role of microbes in biofuels production
For example, methane, ethanol, hydrogen
The role of microbes in cleaning up pollutants (bioremediation)
Microorganisms are important in energy production, including the production of methane (natural gas), energy stored in organisms (biomass), and ethanol.
Biotechnology is the use of microorganisms in industrial biosynthesis, typically by microorganisms that have been genetically modified to synthesize products of high commercial value.
Various microorganisms can be used to consume spilled oil, solvents, pesticides, and other environmentally toxic pollutants.
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27. Figure 1.11
Figure 1.11 Biofuels.
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28. 1.5 The Impact of Microorganisms on Humans
Microorganisms and Their Genetic Resources
Exploitation of microbes for production of antibiotics, enzymes, and various chemicals
Genetic engineering of microbes to generate products of value to humans, such as insulin (biotechnology)
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29. 1.5 The Impact of Microorganisms on Humans
Microbiology as a Career
Clinical medicine
Research and development – pharmaceutical, chemical/biochemical, biotechnology
Microbial monitoring in food and beverage industries, public health, government
“The role of the infinitely small in nature is infinitely large” – Louis Pasteur
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30. II. Pathways of Discovery in Microbiology
1.6 The Historical Roots of Microbiology
1.7 Pasteur and the Defeat of Spontaneous Generation
1.8 Koch, Infectious Disease, and Pure Culture Microbiology
1.9 The Rise of Microbial Diversity
1.10 The Modern Era of Microbiology
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31. 1.6 The Historical Roots of Microbiology
Microbiology began with the microscope (Figure 1.12a)
Robert Hooke (1635–1703): the first to describe microbes
Illustrated the fruiting structures of molds (Figure 1.12b)
Antoni van Leeuwenhoek (1632–1723): the first to describe bacteria (Figure 1.13)
Further progress required development of more powerful microscopes
Ferdinand Cohn (1828–1898): founded the field of bacterial classification and discovered bacterial endospores
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32. Figure 1.12 Figure 1.12 Robert Hooke and early microscopy.
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33. Lens Figure 1.13 Figure 1.13 The van Leeuwenhoek microscope.
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34. 1.7 Pasteur and the Defeat of Spontaneous Generation
Louis Pasteur (1822–1895)
Discovered that living organisms discriminate between optical isomers
Discovered that alcoholic fermentation was a biologically mediated process (originally thought to be purely chemical)
Disproved theory of spontaneous generation (Figure 1.16)
Led to the development of methods for controlling the growth of microorganisms (aseptic technique)
Developed vaccines for anthrax, fowl cholera, and rabies
Spontaneous generation was the hypothesis that living organisms can originate from nonliving matter. Pasteur disproved this idea through a famous experiment (Figure 1.13) in which he compared the growth of microorganisms in one flask containing sterile broth that was exposed to the air and one containing sterile broth that was not exposed to the air.
Microorganisms grew only in the flask exposed to the air, thereby refuting the idea that cells can arise spontaneously from nonliving matter.
Pasteur’s Experiment
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35. Steam, forced out open end
Figure 1.16a
Steam, forced out open end
Figure 1.16 The defeat of spontaneous generation: Pasteur’s swan-necked flask experiment.
Nonsterile liquid poured into flask
Neck of flask drawn out in flame
Liquid sterilized by extensive heating
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36. Dust and microorganisms trapped in bend Open end
Figure 1.16b
Dust and microorganisms trapped in bend
Open end
Long time
Figure 1.16 The defeat of spontaneous generation: Pasteur’s swan-necked flask experiment.
Liquid cooled slowly
Liquid remains sterile indefinitely
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37. Flask tipped so microorganism-laden dust contacts sterile liquid
Figure 1.16c
Short time
Flask tipped so microorganism-laden dust contacts sterile liquid
Liquid putrefies
Figure 1.16 The defeat of spontaneous generation: Pasteur’s swan-necked flask experiment.
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38. 1.8 Koch, Infectious Disease, and the Rise of Pure Cultures
Robert Koch (1843–1910)
Demonstrated the link between microbes and infectious diseases
Identified causative agents of anthrax and tuberculosis
Koch’s postulates (Figure 1.19)
Developed techniques (solid media) for obtaining pure cultures of microbes, some still in existence today
Awarded Nobel Prize for Physiology and Medicine in 1905
Koch’s Postulates
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39. KOCH’S POSTULATES Figure 1.19 The Postulates: Tools:
Diseased animal
Healthy animal
The Postulates:
Tools:
1. The suspected pathogen must be present in all cases of the disease and absent from healthy animals.
Microscopy, staining
Red blood cell
Observe blood/tissue under the microscope
Red blood cell
Suspected pathogen
2. The suspected pathogen must be grown in pure culture.
Laboratory culture
Streak agar plate with sample from either diseased or healthy animal
No organisms present
Colonies of suspected pathogen
Inoculate healthy animal with cells of suspected pathogen
3. Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal.
Experimental animals
Figure 1.19 Koch’s postulates for proving cause and effect in infectious diseases.
Diseased animal
Remove blood or tissue sample and observe by microscopy
4. The suspected pathogen must be reisolated and shown to be the same as the original.
Laboratory reisolation and culture
Suspected pathogen
Laboratory culture
Pure culture (must be same organism as before)
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40. 1.8 Koch, Infectious Disease, and Pure Culture Microbiology
Koch’s Postulates Today
Koch’s postulates apply for diseases that have an appropriate animal model
Remain “gold standard” in medical microbiology, but not always possible to satisfy all postulates for every infectious disease
Animal models not always available
For example, cholera, rickettsias, chlamydias
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41. 1.8 Koch, Infectious Disease, and Pure Culture Microbiology
Koch and the Rise of Pure Cultures
Discovered that using solid media provided a simple way of obtaining pure cultures
Began with potato slices, but eventually devised uniform and reproducible nutrient solutions solidified with gelatin and agar
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42. 1.9 The Rise of Microbial Diversity
Field that focuses on nonmedical aspects of microbiology
Roots in 20th century
Martinus Beijerinck (1851–1931)
Developed enrichment culture technique
Microbes isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions
Example: nitrogen-fixing bacteria (Figure 1.21)
Beijerinck and Winogradsky studied bacteria in soil and water and developed the enrichment culture technique for the isolation of representatives of various physiological groups
Major new concepts in microbiology emerged during this period, including enrichment cultures, chemolithotrophy, chemoautotrophy, and nitrogen fixation.
Martinus Beijerinck, professor at the Delft Polytechnic School in Holland, trained as a botanist. Began career in microbiology studying plants.
Sergei Winogradsky, Russian microbiologist, contemporary of Beijerinick.
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43. Figure 1.21 Figure 1.21 Martinus Beijerinck and Azotobacter.
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44. 1.9 The Rise of Microbial Diversity
Sergei Winogradsky (1856–1953) and the Concept of Chemolithotrophy
Demonstrated that specific bacteria are linked to specific biogeochemical transformations (e.g., S & N cycles)
Proposed concept of chemolithotrophy
Oxidation of inorganic compounds linked to energy conservation
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45. 1.10 The Modern Era of Microbiology
In the 20th century, microbiology developed in two distinct directions:
Applied and basic
Molecular microbiology
Fueled by the genomics revolution
In the middle to latter part of the twentieth century, basic and applied microbiology worked hand in hand to usher in the current era of molecular microbiology.
Table 1.1 summarizes some of the important discoveries in the field of microbiology, from van Leeuwenhoek to the present.
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46. 1.10 The Modern Era of Microbiology
Major Subdisciplines of Applied Microbiology
Medical microbiology and immunology
Have roots in Koch’s work
Agricultural microbiology and industrial microbiology
Developed from concepts developed by Beijerinck and Winogradsky
Aquatic microbiology and marine microbiology
Developed from advances in soil microbiology
Microbial ecology
Emerged in 1960s–70s
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47. 1.10 The Modern Era of Microbiology
Basic Science Subdisciplines in Microbiology
Microbial systematics
The science of grouping and classifying microorganisms
Microbial physiology
Study of the nutrients that microbes require for metabolism and growth and the products that they generate
Cytology
Study of cellular structure
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48. 1.10 The Modern Era of Microbiology
Basic Science Subdisciplines in Microbiology
Microbial biochemistry
Study of microbial enzymes and chemical reactions
Bacterial genetics
Study of heredity and variation in bacteria
Virology
Study of viruses
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49. 1.10 The Modern Era of Microbiology
Molecular Microbiology
Biotechnology
Manipulation of cellular genomes
DNA from one organism can be inserted into a bacterium and the proteins encoded by that DNA harvested
Genomics: study of all of the genetic material (DNA) in living cells
Transcriptomics: study of RNA patterns
Proteomics: study of all the proteins produced by cell(s)
Metabolomics: study of metabolic expression in cells
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