Chapter One

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Chapter One

• Microorganisms and Microbiology

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What is Microbiology?

• Study of microorganisms
• Microorganisms can include single celled
  organisms and viruses
• Generally too small to be seen with naked eye
• Microscopic
• Have enormous impact
• Divided into six subgroups
• Bacteria (Bacteriology)
• Archaea
• Fungi (Mycology)
• Protozoa (parasitology)
• Algae (phycology)
• Viruses (virology)
• Helminths (parasitology)

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Classification of Microorganisms
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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

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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

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Microbiology

• Foundation of all the biological sciences
• First organisms on the planet
• Basic Microbiology
• Understanding Life
• Applied Microbiology
• Human needs
• More BENEFICIAL effect than harmful
• Environment
• Oxygen generation
• Decomposition
• Health/Medicine
• Protection from disease
• Biotechnology
• Food
• Agriculture
• Products
• BAD Bacteria!
• Plant and animal diseases
• Rusting

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The Cell

• Fundamental unit of life
• Major components
• Cell (cytoplasmic) Membrane
• Barrier that separates the inside of the cell
  from the outside environment
• Constant communication
• Cells always change physiology
• Cytoplasm
• Fluid that fills cells
• Nucleus (or nucleoid)
• Genetic material (DNA or RNA)
• Machinery for cell growth and function
• Ribosomes
• Protein synthesis
• Organic macromolecules
• Proteins, nucleic acids, lipids and
  polysaccharides
• Cell Wall
• Present in most microbes, confers structural
  strength
• What are the characteristics of life?

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The Characteristics of Cellular Life
Figure 1.3
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The Characteristics of Cellular Life
Figure 1.3
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The Characteristics of Cellular Life
Figure 1.3
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Cells

• As Machines
• Carry out chemical transformations using enzymes
  (catalysts)
• As Coding Devices
• Store and process genetic information (DNA) that
  is passed on to offspring
• Growth
• The link between cells as machines and cells as
  coding devices

Figure 1.4
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How do microorganisms exist?

• 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

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Microbial Ecology

• Study of microorganisms in their natural habitat
• Individual cell
• Make up tissues in a multicellular organism
• In a unicellular organism, the cell is the entire
  organism
• Population
• Interacting group of individuals of one species
• A group of related cells derived from a parent
  cell
• A microbial habitat is the location in an
  environment where a microbial population lives
• Community
• All the organisms inhabiting an ecosystem
• SO, a microbial community are many different
  populations of microorganisms occupying the same
  habitat
• Ecosystem
• Communities of organisms and their natural
  environment
• All the organisms living within a particular area
  and the nonliving, physical components of the
  environment in which the organisms interact

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Individual cell
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1.3 Microorganisms and 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

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1.4 The Antiquity and Extent of Microbial Life

• 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

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1.4 The Antiquity and Extent of Microbial Life

• 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)

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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

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Impact of Microorganisms

• Microorganisms as Disease Agents
• Control of infectious disease during last century
  (Figure 1.8)

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Impact of Microorganisms

• Microorganisms and Agriculture
• Many aspects of agriculture depend on microbial
  activities
• Nitrogen-fixing bacteria produce usable nitrogen
  for plants to use for growth
• Cellulose-degrading microbes in the rumen
• In cattle and sheep, microorganisms carry out the
  digestion of cellulose
• Regeneration of nutrients in soil and water

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Microorganisms can have both positive and
negative effects on food

• Negative impacts
• Food can become contaminated by microorganisms
• 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)

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Microorganisms are important in energy production

• Natural gas (methane) is a product of bacterial
  activity
• Waste materials can be converted to biofuels by
  microorganisms
• e.g., methane, ethanol, hydrogen
• Microorganisms can detoxify unwanted wastes in
  the environment
• Bioremediation The role of microbes in cleaning
  up pollutants

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E. Coli is an important microorganism for genetic
engineering

• 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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History of Microbiology
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History of Microbiology

• Discovery
• Robert Hooke (1665) was the first to describe
  microbes
• Illustrated the fruiting structures of molds
• Led to the Cell Theory
• All living things consist of cells
• Cells are the smallest unit of life maintaining
  properties of life
• Life continues because of growth and division of
  cells
• Antoni Van Leeuwenhoek (late 1600s)
• Was the first to describe bacteria
• Microscopic organisms - Animalcules
• Submitted findings to Royal Society of London
• Raised questions Where did they originate?

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Robert Hooke and Early Microscopy
Figure 1.9b
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Leeuwenhoeks lens
Leeuwenhoeks animalcules
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19th century Ferdinand Cohn

• Botanist who thought that algae and
  photosynthetic bacteria were plants
• Founded the field of bacteriology
• Discovered Bacillus and endospores were heat
  resistant
• Developed sterilization for microbial media
• Cotton closures for liquid cultures
• Helped Robert Koch develop the aseptic technique

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Spontaneous Generation

• Life formed spontaneously from non-living matter
• Believed to be the origin of animalcules
• Louis Pasteur (1861)
• Experiments disproving spontaneous generation
• Led to the development of aseptic techniques

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The Defeat of Spontaneous Generation Pasteurs
Experiment
Figure 1.13a
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The Defeat of Spontaneous Generation Pasteurs
Experiment
Figure 1.13b
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The Defeat of Spontaneous Generation Pasteurs
Experiment
Figure 1.13c
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Golden Age of Microbiology (1857- 1914)

• Period of rapid development
• Pasteur
• Disproved spontaneous generation
• S-shaped necked flask experiments
• Additional work
• Fermentation
• Discovered that alcoholic fermentation was a
  biologically mediated process (originally thought
  to be purely chemical)
• Pasteurization
• Silk worm disease
• Developed vaccines for anthrax, fowl cholera, and
  rabies

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Robert Koch

• Germ theory of disease
• Robert Koch (1876)
• First medical microbiologist
• Proved germ theory of disease
• Definitively demonstrated the link between
  microbes and infectious diseases
• Discovered Bacillus anthracis
• Identified causative agents of anthrax and
  tuberculosis
• Showed Mycobacterium tuberculosis causes TB
• Mycobacterium tuberculosis difficult to stain
  because of a waxy lipid present in the cell wall
• Developed precursor to the acid fast stain
• Kochs postulates
• Developed a set of postulates to prove that a
  specific microorganism causes a specific disease

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Kochs postulates

• Organism present only in diseased individuals
• Organism cultivated in pure culture from diseased
  individual

Figure 1.15
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Kochs postulates

• Organism causes disease when injected into
  healthy individuals
• Organism re-isolated from infected individual
  from point 3.

Figure 1.15
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Best Way to study microorganisms

• Koch developed techniques (solid media) for
  obtaining pure cultures of microbes, some still
  in existence today
• Pure culture
• A population of cells that all come from a single
  cell
• Broth or agar
• Laboratory population
• Need proper nutrient media and environmental
  conditions

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Rise of General Microbiology

• 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
• Isolated many types of bacteria from the
  environment

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Winogradsky (1856-1953)

• Studied physiological processes
• Nitrification
• H2S oxidation
• Nitrogen fixation
• Nitrifying bacteria
• Coined the terms chemolithotrophy (trap energy
  available in inorganic compounds) and autotrophy
  or chemoautotroph (use CO2 as a source of carbon)

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Winogradsky
Figure 1.19a
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Winogradsky
Figure 1.19b
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Microbiology Research Today

• Genome sequencing, bioinformatics and proteomics
  (biocomputing)
• Phylogeny (renaming, reclassifying and
  determining evolutionary trends)
• Characterizing novel organisms
• AIDS
• Discovering antibiotics and understanding
  antibiotic resistance
• Medical microbiology new treatment for diseases
  and understanding diseases
• Bioremediation use microorganisms to remove
  toxic or unwanted chemicals in an environment
  clean up pollution created by humans