1ch01 Lecture

Brock Biology of Microorganisms
Twelfth Edition
Madigan / Martinko Dunlap / Clark
Chapter 1
Microorganisms and Microbiology
Lectures by Buchan & LeCleir
Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings
1.1 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) Application of that understanding to benefit of humans

Microbes play important roles in medicine, agriculture, and industry
1.1 Microbiology
The Importance of Microorganisms
Oldest form of life
Largest mass of living material on Earth

Carry out major processes for biogeochemical cycles
1.2 Microorganisms as Cells

The Cell
A dynamic entity that forms the fundamental unit of life Four classes of cellular macromolecules
Proteins Nucleic acids Lipids Polysaccharides
Rod-shaped Bacterial Cells
Figure 1.2

Cell Chemistry and Key Structures
Cytoplasmic (cell) membrane
Barrier that separates the inside of the cell from the outside environment
Cytoplasm
Fluid that fills cells
Nucleus or nucleoid and ribosomes

Machinery for cell growth and function
Cell wall
Present in most microbes, confers structural strength

Characteristics of Living Systems
Compartmentalization and Metabolism: chemical transformation of nutrients
Regeneration: repair and replacement of components

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
The Characteristics of Cellular Life
Figure 1.3
Figure 1.3
Figure 1.3

Cells as Machines and as Coding Devices
(1) Cells can be considered machines that carry out chemical transformation
Enzymes: protein catalysts of this chemical machine; accelerate the rate of chemical reactions
(2) Cells can also be considered coding devices that store and process information that is eventually passed on to offspring during reproduction through DNA (deoxyribonucleic acid) and evolution
Growth
The link between cells as machines and cells as coding devices
The Machine and Coding Functions of the Cell
Figure 1.4 Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings
1.3 Microorganisms and Their Natural Environments

Microorganisms exist in nature in populations of interacting
assemblages called microbial communities

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 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

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
e.g., removal of nutrients from the environment and the excretion of waste products
1.4 The Antiquity and Extent of Microbial Life

The First Cells
First self-replicating entities may not have been cells Universal ancestor: common ancestral cell from which all
cells descended

Life on Earth through the Ages
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
A Summary of Life on Earth Through Time
Figure 1.6

The Extent of Microbial Life
Microbes found in almost every environment imaginable Global estimate of 5 x 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)
The Impact of Microorganisms on Humans
Figure 1.7
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) But many more microorganisms in nature are beneficial
than are harmful
Microorganisms as Disease Agents

Control of infectious disease during last century (Figure 1.8)
Figure 1.3
Death Rates and the Leading Causes of Death in the U.S.
Figure 1.8

Microorganisms and Agriculture
Many aspects of agriculture depend on microbial
activities
Nitrogen-fixing bacteria Cellulose-degrading microbes in the rumen Regeneration of nutrients in soil and water

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, Energy, and the Environment
The role of microbes in biofuels production
e.g., methane, ethanol, hydrogen
The role of microbes in cleaning up pollutants

(bioremediation)
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)

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
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 the Rise of Pure
Culture Microbiology
1.9 Microbial Diversity and the Rise of General Microbiology 1.10 The Modern Era of Microbiology
1.6 The Historical Roots of Microbiology

The Historical Roots of Microbiology
Robert Hooke (1635-1703) was the first to describe
microbes
Illustrated the fruiting structures of molds (Figure 1.9b)
Anton van Leeuwenhoek (1632-1723) was the first to
describe bacteria (Figure 1.10b)

Further progess required development of more powerful microscopes
Ferdinand Cohn (1828-1898) founded the field of

bacteriology and discovered bacterial endospores
Robert Hooke and Early Microscopy
Figure 1.9a
Robert Hooke and Early Microscopy
Figure 1.9b
The van Leeuwenhoek Microscope
Figure 1.10
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 1.13)
Led to the development of methods for controlling the growth of microorganisms
Developed vaccines for anthrax, fowl cholera, and rabies

Pasteurs Experiment
The Defeat of Spontaneous Generation: Pasteurs Experiment
Figure 1.13a
Figure 1.13b
Figure 1.13c
1.8 Koch, Infectious Disease, and the Rise of Pure Cultures

Robert Koch (1843-1910)
Definitively demonstrated the link between microbes and infectious diseases
Identified causative agents of anthrax and tuberculosis
Kochs postulates (Figure 1.15) Developed techniques (solid media) for obtaining pure cultures of microbes, some still in existence today
Awarded Nobel Prize for Physiology and Medicine in 1905
Kochs Postulates
Proof that microbes cause disease
1857: Louis Pasteur proposed the "germ theory" of disease.
1867: Joseph Lister (1827-1912) introduced antiseptics in surgery. By spraying carbolic acid
on surgical instruments, wounds and dressings, he reduced surgical mortality due to

bacterial infection considerably.
Kochs Postulates
Figure 1.15
Kochs Postulates
Figure 1.15
1.8 Koch, Infectious Disease, and the Rise of Pure Cultures

Kochs Postulates Today
Can relatively easily prove Kochs postulates for diseases when an appropriate animal model is available Remain gold standard in medical microbiology, but not
always possible to satisfy all postulates for every

infectious disease Animal models not always available
e.g., cholera, rickettsias, chlamydias
Development of methods to grow & study microbes

Culture methods were developed in Robert Kochs lab 1870-81 potato slices gelatin on glass plates Agar as a solidifying agent at the suggestion of Fanny Hesse,
wife of Kochs colleague
Development of methods to grow & study microbes
Christian Gram, 1884 Gram stain
R J Petri, 1887- Petri dish
1.9 Microbial Diversity and the Rise of General Microbiology

General Microbiology
Field that focuses on non-medical 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 e.g., Nitrogen-fixing bacteria
1.9 Microbial Diversity and the Rise of General Microbiology
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 (Figure 1.19)
Major Concepts Conceived by Sergei Winogradsky
Figure 1.19a
Major Concepts Conceived by Sergei Winogradsky
Figure 1.19b
1.10 The Modern Era of Microbiology

In 20th century microbiology developed in two distinct
directions
Applied and Basic
Origin of the Major Subdisciplines of Applied
Microbiology
Medical Microbiology and Immunology have roots in Kochs 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
Some Landmarks in Molecular Microbiology since 1985
Figure 1.20

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
Microbial Biochemistry Study of microbial enzymes and chemical reactions Bacterial Genetics
Study of heredity and variation in bacteria

Virology
Study of viruses

The Era of Molecular Microbiology
Biotechnology
Manipulation of cellular genomes DNA from one organism can be transplanted into a bacterium and the proteins encoded by the DNA harvested
Genomics: study of all of the genetic material (DNA) in living cells

Proteomics: study of all the proteins produced by cell(s)
Metabolomics: study of metabolic expression in cells
Microbiology sub-disciplines
Basic microbiology research Food microbiology Environmental microbiology/Microbial Ecology Forensic microbiology
Medical microbiology
Biotechnology Academic microbiology Geomicrobiology
The Microbial World
All living things can be classified in one of three groups

Also known as domains
Organisms in each domain share certain properties

These properties distinguish them from organisms in other domains
Three domains are

Bacteria Archea Eucarya
Size of typical bacteria is 0.5 5 mm
The Microbial World

Bacteria and Archaea Both are single-celled organisms Contain no membrane bound nucleus Termed prokaryotes = pre nucleus
Pro = pre
karyote = nucleus
Do not contain any other organelles

Cytoplasm is surrounded by rigid cell wall
The Microbial World

Eucarya Organisms contain membrane bound nucleus
Termed eukaryote = true nucleus
Eu = true
karyote = nucleus
Contains internal organelles

Making organism more complex
Example = mitochondria
May be single or multicellular

Characteristic Chromosome Chromosome shape # chromosome copies Ribosome size
Prokaryote Nucleoid Circular 1- haploid 70S
Eukaryote Nucleus Linear 2 - diploid 80S
Domain Bacteria
Most common type in human infection Members widely diverse Most prominent features include:
Specific shapes
Rod-shaped, spherical and spiral
Rigid cell walls

Responsible for cell shape
Multiply by binary fission

One cell divides into two Each cell is genetically identical to the first
Some bacteria are motile

Move by means of flagella
Domain Archaea
Demonstrate a number of same attributes as Bacteria

Same shapes Multiply through binary fission Move by means of flagellum
Archaea exhibit significant differences

Chemical composition of cell wall differs from organisms in other domains Organisms of Archaea domain found in extreme environments
Extreme temperatures Environments with high concentrations of salts
Domain Eucarya
All members are eukaryotic Microbial world composed of single-celled Eucarya Algae Fungi
Protozoa
Hallmarks of Cellular Life
Metabolism Reproduction/growth Differentiation spores, etc Cellular Communication Quorum Sensing Movement / Motility Evolution / Genetic Change
Viruses, Viroids, Prions

Non-living elements Called agents Not organisms Usually consist of only a few molecules found in living cells
Viruses
Viruses contain protein coat surrounding nucleic acid (DNA or RNA, ss or ds)
Shape is helical
or icosohedrial
Naked or enveloped
(from membrane of host cell)
Viroids
Viroids are simpler than viruses Still require host cell for replication Consist of a single short piece of RNA Contain no protective protein coat
Viroids smaller than viruses

Generally cause plant diseases
Prions
Prions are infectious proteins Contain no nucleic acid Responsible for six neurodegenerative diseases Animal disease Scrapie in sheep Mad cow disease in cattle Human disease Kuru Creutzfelt-Jakob
Size in the Microbial World
Tremendous range in size

Smallest virus approximately 1/1,000,000th size of largest
eukaryotic cell

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Brock Biology of Microorganisms

Madigan / Martinko Dunlap / Clark

(2) Application of that understanding to benefit of humans

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Largest mass of living material on Earth

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.2 Microorganisms as Cells

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Rod-shaped Bacterial Cells

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.2 Microorganisms as Cells

Nucleus or nucleoid and ribosomes

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.2 Microorganisms as Cells

Regeneration: repair and replacement of components

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.2 Microorganisms as Cells

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

The Characteristics of Cellular Life

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

The Characteristics of Cellular Life

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

The Characteristics of Cellular Life

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.2 Microorganisms as Cells

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.2 Microorganisms as Cells

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

The Machine and Coding Functions of the Cell

1.3 Microorganisms and Their Natural Environments

assemblages called microbial communities

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.3 Microorganisms and Their Natural Environments

The activities of microbial communities can affect the

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.3 Microorganisms and Their Natural Environments

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.4 The Antiquity and Extent of Microbial Life

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.4 The Antiquity and Extent of Microbial Life

Life was exclusively microbial until ~1 billion years ago

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

A Summary of Life on Earth Through Time

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.4 The Antiquity and Extent of Microbial Life

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

The Impact of Microorganisms on Humans

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.5 The Impact of Microorganisms on Humans

Emphasis typically on harmful microorganisms

than are harmful

Microorganisms as Disease Agents

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Death Rates and the Leading Causes of Death in the U.S.

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.5 The Impact of Microorganisms on Humans

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.5 The Impact of Microorganisms on Humans

Food spoilage by microorganisms requires specialized

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

1.5 The Impact of Microorganisms on Humans

The role of microbes in cleaning up pollutants

Copyright 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings