Naming and Classifying Microorganisms
1735 – Linnaeus – set up binomial nomenclature
Genus + specific epithet = species
Ex. Escherichia
coli
After first citation can use E. coli
Types of Microorganisms (Fig. 1.1)
A. Bacteria
Unicellular
Prokaryotes (no nucleus)
Three shapes
1. Bacillus à rods
2. Coccus à spherical
3. Spiral à corkscrew
Cell walls of peptidoglycan
Produce asexually by binary fission
B. Archaea
Unicellular
Prokaryotes
Some have cell walls (but not of peptidoglycan)
Live in extreme environments
3 groups
1.
Methanogens – produce methane
2. Extreme
halophiles – in very salty environments
3. Extreme
thermophiles – in hot springs
C. Fungi
Unicellular or multicellular
Eukaryotes ( nucleus)
NO photosynthesis
Cell walls of chitin
Reproduce asexually or sexually
Two forms
1. Yeasts –
unicellular
2. Molds –
multicellular, filamentous
D. Protozoa
Unicellular
Eukaryotic
No cell walls
Reproduce sexually or asexually
Can be free living or parasitic
E. Algae
Eukaryotes
Most unicellular
Photosynthetic
Sexual and asexual reproduction
Cell walls of cellulose
F. Viruses
Very small
Acellular
All are parasitic
G. Helminths
Flatworms and Roundworms
Parasitic
Multicellular
Classification of organisms
A. Domain
Bacteria
B. Domain
Archaea
C. Domain
Eukarya
1. Kingdom
Protista (Protozoa and Algae)
2. Kingdom
Fungi
3. Kingdom
Plantae
4. Kingdom
Animalia
History of Microbiology
A. Early
microscopy
1665 – Robert Hooke looks at cork with microscope and
sees cells
1673 – Leeuwenhoek – sees live microbes (Fig 1.2)
B.
Spontaneous generation vs. biogenesis
Spontaneous generation – life can arise spontaneously
from nonliving matter
Biogenesis – living cells can only arise from
preexisting living cells
1668 – Redi – sealed jars of meat had no maggots
1745 – Needham – heated broths, put in covered
flasks, grew microbes
1765 – Spallanzani – heated broth in flask after
sealed à no growth
But others said no growth was due to lack of oxygen
1861 – Louis Pasteur
Swan neck flask experiment (Fig 1.3) à Biogenesis was correct
Also developed aseptic techniques (prevent
contamination by
unwanted microorganisms) and pasteurization.
C. The Germ
theory of disease – microorganisms cause disease
1796 – Jenner – vaccine for smallpox
exposure to cowpox gives immunity to smallpox
1840’s – Semmelweiss
Had physicians wash hands
à drastically cut rates of puerperal fever
1860’s – Lister
Treated surgical wounds with phenol
à Drastically reduced incidence of infections
1876 – Robert Koch
Established Koch’s postulates
à Sequence of experimental steps for directly relating
a specific microbe to a specific disease.
D.
Chemotherapy
1. Synthetic
drugs
1910 – Ehrlich
Developed salvarsan - “magic bullet” for syphilis
1930’s – sulfa drugs
2.
Antibiotics
1928 – Alexander Fleming
Discovered penicillin (Fig. 1.5)
Beneficial activities of Microorganisms
A. Recycling
vital elements
Ex: nitrogen
fixation
B. Sewage
treatment
C.
Bioremediation
Break down toxins
Ex: Exxon
Valdez oil spill cleanup
D. Insect
pest control
Ex: Bacillus
thuringiensis kills agricultural pests
E.
Biotechnology
Producing foods and chemicals
F. Genetic
engineering
Gene therapy – Ex:
replace faulty cystic fibrosis gene,
Develop disease and drought resistance in crops
Relationship of microbes and humans
A. Normal Microbiota (Fig 1.7)
Live on or in our bodies
Beneficial – prevent overgrowth of harmful microbes,
produce vitamins
B. Pathogens
Invade host, carry on life cycle, cause damage to the
host
Emerging infectious diseases (caused by pathogens)
Bovine Spongiform encephalopathy (BSE)
Creutzfeldt-Jakob disease (CJD)
E. coli O157:H7
Invasive Group A Streptococcus “flesh-eating
bacteria”
Ebola
Hantavirus
Acquired Immunodeficiency syndrome (AIDS)
Chapter
3 Observing Microorganisms through a
Microscope
Units of measurement (Table 3.1) Know metric units
and metric equivalents
Microscopy:
The instruments (Fig 3.4) (Table 3.2)
A.
Brightfield Microscopy (Compound Light Microscopy)
See dark object on light background
Usually have to stain to increase contrast
B. Darkfield
Microscopy
Use opaque disc to create light object on a dark
background
Gives better contrast
Use on unstained live specimens
C.
Phase-contrast microscopy
Better contrast
Use on unstained live specimens
Can see internal structures better
D.
Fluorescence Microscopy
Use fluorescent dyes
See glowing objects on dark background
E. Electron
Microscopy
Use electrons rather than light
1000X more magnification and resolution than light
microscopes
1.
Transmission Electron Microscopy
Electrons transmitted though specimen
2-D view
2. Scanning
electron Microscopy
Electrons scattered off surface
3-D view
Relationship between sizes (Fig 3.2)
Preparation of specimens for light microscopy à staining
Stains = salt = Positive ion + negative ion
Only one ion is colored à chromophore
Non-colored ion à auxochrome
DRAW
Types of Staining
A. Negative
staining à chromophore is
negative à uses acidic dyes
DRAW
B. Positive
staining à chromophore is
positive à uses basic dyes
DRAW
Two types of positive staining
1. Simple
staining
Use single dye
Ex: Crystal
violet
2.
Differential staining
Use more than one dye
Used to distinguish different bacteria
Ex: Gram
stain (Crystal violet and Safranin) (Fig. 3.10)
Overview – Prokaryotes vs. Eukaryotes
Prokaryotes
|
Eukaryotes
|
|
No nucleus |
Nucleus |
|
One circular chromosome |
Multiple Chromosomes |
|
No mem. enclosed organelles |
Organelles |
|
Cell wall of peptidoglycan |
Cell wall, when present, is not peptido. |
|
Divide by binary fission |
Divide by mitosis |
The prokaryotic cell
A. Size
.2 – 2.0 mm diameter
2 – 8 mm length
B. Shape
1. Coccus -
spherical
2. Bacillus –
rod shaped
3.
Coccobacilli - oval
4. Spirals
(Fig 4.4)
a. Vibrios –
comma-shaped
b. Spirilla –
corkscrew (rigid)
c.
Spirochetes – corkscrew (flexible)
5.
Pleomorphic – many shapes
C.
Arrangements
1. Coccus
(Fig. 4.1)
a. Diplococci
– pairs
b.
Streptococci – chains
c. Tetrads –
groups of 4
d. Sarcinae –
cube like groups of 8
e.
Staphylococci – grapelike clusters
2. Bacilli
(Fig 4.2)
a.
Diplobacilli – pairs
b. Streptobacilli – chains
3. Spirals –
none
Structure of a typical prokaryotic cell (Fig. 4.6)
A. Structures
external to the cell wall
1. Glycocalyx
– gelatinous layer of polysaccharide and/or polypeptide
a. Capsule
Organized
Firmly attached to cell
Protects cell from host immune cells
b. Slime
layer
Unorganized
Loosely attached
c.
Extracellular polysaccharide
Thin polysaccharide fibers
Use to attach to surfaces
2. Flagella
a.
Arrangements (Fig. 4.6)
(1)
Monotrichous – single polar flagellum
(2)
Amphitrichous – tuft of flagella or single flagella at each end of cell
(3)
Lophotrichous – 2 or more flagella at one pole
(4)
Peritrichous – flagella all over cell
b. Structure
(Fig. 4.8)
Filament
Hook
Basal body
c. Patterns
of motility (Fig. 4.9)
Move by “runs and tumbles”
Runs–flagella rotates one way, run in straight line
Tumbles – flagella rotates opposite way, tumbles
Chemotaxis – movement toward or away from chemical
Phototaxis – movement toward or away from light
3. Axial
Filaments (Fig 4.10)
Flagella inside outer sheath
Corkscrew motion
Seen in spirochetes
4. Fimbriae
Many short hairlike protein appendages
Function:
attachment
5. Pili
Longer protein tube
Function:
transfer DNA from one cell to another
DRAW
B. Cell Wall
1. Function
a. Protect
cell from osmotic lysis
b. Maintain
shape of cell
c. Anchorage
for flagella
2.
Composition (Fig 4.13a)
Made of layers of peptidoglycan either alone or with
other substances
Structure of peptidoglycan
DRAW
3. Types of
cell walls
a.
Gram-positive Cell Walls
DRAW
b.
Gram-Negative cell walls
DRAW
4. Cell walls
and the Gram stain mechanism
a. Crystal
Violet (primary stain) à
stains all cells
b.
Iodine (mordant àintensifies stain)
à forms large CV-I crystals
c. Alcohol
(decolorizer)
à seals off thick cell wall of Gram positive
à destroys outer mem & leaches stain on Gram neg.
d. Safranin –
(counterstain) à
stains Gram negative pink
5. Atypical
cell walls
a. Mycoplasma
– no cell wall
b. Archaea –
no peptidoglycan, some no cell wall
C. Structures
internal to the cell wall
1. Plasma
membrane (Fig 4.14)
a. Structure
Phospholipid bilayer
Proteins
Peripheral proteins
Integral proteins
Fluid mosaic model
DRAW
b. Function
Selective permeability – certain molecules can pass through, others cannot
2. Cytoplasm
– substance inside the plasma membrane
a. Nucleoid
Location of bacterial chromosome
b. Plasmids
Small circular DNA molecules
Have 5 to 100 genes
Can carry genes for antibiotic resistance and toxin
prod.
c. Ribosomes
(Fig. 4.19)
Sites of protein synthesis
Composed of protein and rRNA
70s (eukaryotic ribosomes are 80s)
d. Inclusions
– deposits in cell
(1)
Metachromatic (volutin) granules
Source of phosphate used to make ATP
(2) Polysaccharide
granules
Consist of glycogen or starch
Used for energy storage
(3) Lipid
inclusions
Usually poly-β-hydroxybutyric acid (PHB)
à unique to bacteria, used for energy storage
(4)
Magnetosomes (Fig. 4.20)
Iron oxide
Act like magnet
D. Endospores
Dehydrated cells with thick wall
Not a reproductive process
Survival structure
à resistant to heat, drying, chemicals, radiation
à can survive boiling for 19 hours
Seen in the genera Bacillus and Clostridium
Ex: Bacillus
anthracis à
causes anthrax
Clostridium tetani à causes tetanus
Sporulation – triggered by nutrient depletion (Fig.
4.21)
1. Spore
septum begins to form
2. Plasma
membrane surrounds DNA
3. Spore
septum surround isolated portion
4.
Peptidoglycan layer forms
5. Spore coat
forms
6. Endospore
freed from cell
Germination
Occurs when conditions turn favorable
Return to vegetative state
25 million year old endospores in amber have
germinated