MICROBIOLOGY

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INTRODUCTION TO
MICROBIOLOGY
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WHAT WILL WE COVER?

• History of microbiology
• Importance of microorganisms
• Classification Unity and diversity of life
• Overview of the main groups of microorganisms
• Size in the microbial world

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MICROORGANISMS

• Existed for majority of Earths history
• Earth 4.5 billion years old
• Microorganisms 3.8 billion years old
• Present in fossil record
• Evolutionary ancestors of all past and present
  life
• Present virtually everywhere
• Very diverse
• Highly adaptable

Fossil Cyanobacteria
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AGE OF EARTH AND LIFE
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DISCOVERY OF CELLS

• Robert Hooke (1665)
• England
• Constructed a microscope
• Viewed microscopic structure of cork
• Named the repeating subunits he viewed cells

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DISCOVERY OF CELLS

• Antony Van Leeuwenhoek (1676)
• Father of Microbiology
• Holland
• Constructed a microscope
• 300X magnification
• Greater resolving power than Hookes microscope
• Viewed bacteria other microorganisms
• animalcules

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ORIGINS OF MICROORGANISMS

• Microorganisms appear, seemingly from nowhere
• Are these microorganisms spontaneously generated?
• Predominant view until 100 years ago
• Disproven by experiments by Pasteur and others
• All life arises from preexisting life

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ORIGIN OF LIFE

• If all life arises from preexisting life, how did
  life originate?
• Life arose on a young Earth
• Earth is 4.5 billion years old, life is 3.8
  billion years old
• Atmospheric conditions very different in early
  Earth
• H2O, H2, NH3, CH4, no free O2
• Conditions recreated in Miller apparatus
• Stanley Miller, 1953 (USA)
• All four main types of macromolecules formed
• All twenty amino acids
• sugars
• lipids
• Nitrogenous bases

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MILLER APPARATUS
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ORIGIN OF LIFE

• What were the earliest microorganisms?
• Not preserved
• Tolerated extreme environment
• High temperature
• No oxygen
• High ultraviolet light
• Mutagenic (damaging to DNA)
• Similar to modern extremophiles?

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MICROORGANISMS

• Helpful or harmful?
• Some microorganisms are parasites or infectious
  agents
• Some, not most
• Responsible for more deaths than all wars
  combined
• Some microorganisms are vital to life
• We could not survive without microorganisms

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IMPORTANCE OF MICROBES

• OXYGEN PRODUCTION
• Atmospheric oxygen (O2) is essential to many
  living things
• O2 must be replaced as it is consumed
• O2 is a product of photosynthesis
• Some O2 is produced by plants
• Most of the Earths O2 is produced by
  microorganisms

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IMPORTANCE OF MICROBES

• CARBON FIXATION
• Carbon firms the skeleton of all organic
  molecules
• Cellular respiration converts organic carbon into
  carbon dioxide (CO2)
• CO2 is unusable by most living things
• Photosynthesis converts CO2 into organic carbon
• Most carbon fixation is accomplished by
  microorganisms

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IMPORTANCE OF MICROBES

• NITROGEN FIXATION
• Nitrogen is an essential component of many
  biologically important molecules
• Almost 80 of the air we breathe is nitrogen gas
  (N2)
• N2 is unusable by most living things
• Only microorganisms can convert atmospheric
  nitrogen to usable forms
• Nitrogen fixation

Rhizobium on clover root
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IMPORTANCE OF MICROBES

• DECOMPOSITION
• Over half of the biospheres organic carbon is
  in the form of cellulose
• Unavailable to most living things
• Can be broken down and used by various
  microorganisms
• e.g., Fungi
• e.g., Symbiotic bacteria in the stomach of
  ruminants (cattle, seep, etc.)
• e.g., Symbiotic bacteria in the gut of termites

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IMPORTANCE OF MICROBES

• FOOD PRODUCTION
• Various microorganisms ferment milk to produce
  cheese yogurt
• Yeast ferment grains fruit to produce beer
  wine
• Yeast makes bread rise

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IMPORTANCE OF MICROBES

• SEWAGE TREATMENT
• Sewage and wastewater are nutrient-rich
• Excess nutrients can cause eutrophication
• Various microbes are used to treat wastewater
• Nutrients are removed and recycled

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IMPORTANCE OF MICROBES

• PRODUCT SYNTHESIS
• Cellulose
• Hydroxybutyric acid ? plastics
• Ethanol
• Insecticides
• Antibiotics
• Amino acids
• Etc.

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IMPORTANCE OF MICROBES

• GENETIC ENGINEERING
• Introduction of foreign genes ( new properties)
  into organisms
• Pharmaceutical production
• Insulin, growth hormone, etc.
• Vaccine production
• Modified crop plants
• Insect resistance, herbicide tolerance, vaccine
  production, altered nutrition, etc.
• Gene therapy
• Delivery of DNA as a drug
• Permanent correction of genetic defects

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IMPORTANCE OF MICROBES

• BIOREMEDIATION
• Degradation of environmental pollutants
• PCBs
• DDT
• Petroleum spills
• Etc.
• Can be enhanced by selection and by genetic
  engineering

COMPLEMENTS OF EXXON VALDEZ
UNCLEANED
CLEANED
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IMPORTANCE OF MICROBES

• BASIC SCIENCE MODEL ORGANISMS
• Display fundamental genetic metabolic
  properties of life
• Easier to study than many other forms of life
• Knowledge applicable to other forms of life

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IMPORTANCE OF MICROBES

• MEDICAL MICROBIOLOGY
• Some microorganisms cause disease
• e.g., smallpox, bubonic plague, leprosy, etc.
• 1918 influenza epidemic caused more deaths than
  WWI, WWII, the Korean War, the Vietnam War
  combined
• Our understanding of disease-causing
  microorganisms has reduced disease incidence
• Sanitation
• Vaccination
• Antibiotics

Rubella (German measles)
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IMPORTANCE OF MICROBES

• MEDICAL MICROBIOLOGY
• New emerging diseases
• Acquired Immunodeficiency Syndrome (AIDS HIV)
• Cryptosporidiosis (Cryptosporidium protozoan)
• Hantavirus Pulmonary Syndrome (Hantavirus)
• Hemolitic-Uremic Syndrome (E. coli bacterium)
• Hemorrhagic Fever (Ebola Marburg viruses)
• Legionnaires Disease (Legionella bacterium)
• Lyme Disease (Borellia bacterium)
• Toxic Shock Syndrome (Staph aureus bacterium)

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EMERGING DISEASES
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IMPORTANCE OF MICROBES

• MEDICAL MICROBIOLOGY
• Why are there new emerging diseases?
• Microbial evolution
• Very rapid
• Human population expansion
• Increased contact with disease reservoirs
• Mass production/storage/distribution of food
• Increase vectors, raid spread
• Changes in human behavior technology
• e.g., daycare centers, contact lenses, tampons
• Etc.

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IMPORTANCE OF MICROBES

• MEDICAL MICROBIOLOGY
• Why are old diseases reappearing?
• Evolution of drug resistance
• Increased international travel
• Complacency regarding vaccinations
• Weaker immune system near end of longer life
• Etc.

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UNIFYING FEATURES OF LIFE

• Composed of cell(s)
• Require energy
• Possess genetic material (DNA)
• Reproduce
• Evolve (populations)
• Etc.
• Though life is diverse, there exists significant
  unity

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CLASSIFICATION

• Organisms are arranged into related groups
• Taxonomic groupings are based on similarities
• Morphological similarities
• Physiological / biochemical similarities
• Genetic similarities
• Taxonomic groupings reflect evolutionary
  relatedness
• A specific scientific name is assigned for each
  species
• (Some convenient non-taxonomic groupings do not
  reflect evolutionary relationships)
• e.g., soil bacteria, intestinal flora, etc.

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CLASSIFICATION

• All living things can be classified into three
  domains
• Archaea
• Bacteria
• Eukarya
• Microorganisms are represented in all three of
  these domains

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CLASSIFICATION

• DOMAINS BACTERIA ARCHAEA
• Prokaryotes
• Lack membrane-bound nucleus and other
  membrane-bound organelles
• Reproduce by binary fission
• Three main cell shapes
• Spherical (cocci)
• Rod-shaped (bacilli)
• Spiral (spirilla/spirochetes)
• Possess rigid cell wall
• Some move via flagella

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CLASSIFICATION

• DOMAIN BACTERIA
• Cell wall contains the compound peptidoglycan
• unique to bacteria
• Best studied prokaryotic domain

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CLASSIFICATION

• DOMAIN ARCHAEA
• Ancient
• Cell wall lacks peptidoglycan
• Other chemical differences
• Able to grow in very adverse environments

Methanosarcina
Sulfur hot spring
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CLASSIFICATION

• EUKARYA
• Eukaryotes
• Unicellular or multicellular
• Possess membrane-bound nucleus and other
  membrane-bound organelles
• Main groups
• Algae
• Fungi
• Protozoa
• Helminths

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CLASSIFICATION

• ALGAE
• Unicellular or multicellular
• Chlorophyll
• Green pigment
• Often other pigments also
• Harvest sunlight (photosynthesis)
• Photoautotrophs
• Produce O2
• Rigid cell walls
• Different from those of bacteria
• Some move via eukaryotic flagella
• More complex than prokaryotic flagella

Volvox
Red coral algae
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CLASSIFICATION

• FUNGI
• Unicellular or multicellular
• e.g., yeasts, molds, mushrooms
• Heterotrophs
• Obtain energy from organic molecules
• Rigid cell walls
• Different from those of bacteria and algae

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CLASSIFICATION

• PROTOZOA
• Unicellular and microscopic
• Lack cell wall
• Shape defined by structures beneath plasma
  membrane
• Most are heterotrophs
• Most move via
• Eukaryotic flagella
• Cilia
• Pseudopods

Paramecium
Amoeba
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CLASSIFICATION

• HELMINTHS
• Multicellular and macroscopic
• Included due to importance as disease-causing
  organisms
• Parasites
• Derive nutrients from host organism
• Three groups
• Roundworms
• Tapeworms
• Flukes

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NON-CELLULAR INFECTIOUS AGENTS

• Viruses
• Viroids
• Prions
• All are obligate intracellular parasites

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VIRUSES
?

• Blur the boundary between life and non-life
• Share some of the unifying features of life
• Differ from normal life in some of these
  characteristics
• Are they alive?
• The answer to this question depends on the exact
  definition of life

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VIRUSES

• CELLULAR LIFE
• Composed of cell(s)
• Require energy
• Genetic material (DNA)
• Reproduction
• Evolution (populations)
• Etc.

• VIRUSES
• Not cellular
• Only when infecting
• DNA or RNA
• Only within host
• Very rapid evolution

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VIRUS STRUCTURE

• SIMPLEST VIRUSES
• naked viruses
• naked nucleocapsid
• Genetic material
• DNA or RNA
• Single- or double-stranded
• Protein coat
• capsid
• Surrounds nucleic acid

Adenovirus
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VIRUS STRUCTURE

• ENVELOPED VIRUSES
• Genetic material
• Protein coat
• Envelope
• Phospholipid bilayer
• External to nucleocapsid
• Integral proteins

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VIROIDS

• Similar, but simpler than viruses
• Genetic material
• Single short piece of RNA
• No protein coat
• Cause disease in plants
• Cause disease in humans???

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PRIONS

• Discovered by Stanley Prusiner (1982)
• Nobel prize in 1997
• Cause disease in humans animals
• Spongiform encephalopathies
• e.g., Mad Cow Disease, Scrapie, Kuru, etc.
• Degeneration of brain structure function
• Always fatal
• Comprised exclusively of protein
• No nucleic acid!!!!!!!!!!!!!!!!!!!!!!!
• Protein alters folding ( shape) of other
  proteins normally present in brain

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MICROORGANISMS

• Prokaryotes
• Bacteria
• Archaea
• Eukaryotes
• Algae
• Fungi
• Protozoa
• Helminths
• Non-cellular infectious agents
• Viruses
• Viroids
• Prions

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TAXONOMIC HIERARCHIES

• All living things are classified into three
  domains
• Each domain is further subdivided
• Each subdivision is further subdivided

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CLASSIFICATION REVISITED

• DOMAIN Bacteria Eukarya
• KINGDOM Animalia
• PHYLUM Proteobacteria Chordata
• CLASS Gammaproteobacteria Mammalia
• ORDER Enterobacteriales Primata
• FAMILY Enterobacteriacaea Hominidae
• GENUS Escherichia Homo
• SPECIES coli sapiens
• STRAIN e.g., K12, O157H7, etc.

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BINOMIAL NOMENCLATURE

• Two word naming system
• Genus species
• e.g., Homo sapiens (H. sapiens)
• e.g., Escherichia coli (E. coli)
• e.g., Bufonaria borisbeckeri (B. borisbeckeri)
• strains are variants within a species
• e.g., E. coli strain K12

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SIZE SIZE SIZE SIZE SIZE

• HOW SMALL IS SMALL?
• Most microorganisms are small
• Small encompasses several orders of magnitude
• Some small organisms are huge in comparison to
  other small organisms
• Be aware of relative differences in size amongst
  microorganisms

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SIZE SIZE SIZE SIZE SIZE