I. Microorganism Diversity

A. Bacteria 1. Constitute a large domain of prokaryotic microorganisms 2. Are unicellular, filamentous, or colonial 3. Typically they a few micrometers in length 4. They have a wide range of shapes, ranging from rods, to spheres and spirals 5. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet 6. They have cell walls composed of peptidoglycan

B. Archaea

1. In the past they were included as a type of bacteria because they are similar in size and shape 2. Are unicellular, filamentous, or colonial 3. Archaea were among the first life forms to appear on Earth, and are present in most habitats on the planet 4. Many members are “extreme” microorganisms -hyperthermophiles -extreme halophiles -methanogens 5. They have cell walls that lack peptidoglycan

C. Fungi 1. Unicellular, filamentous and multicellular 2. Eukaryotic -complex in structure -membrane-bound nucleus -membrane-bound organelles 3. Includes the molds, yeast, mushrooms 4. Cell wall composed of chitin 5. Reproduce by spores and budding 6. Nutrition by absorption

D. Algae

1. Unicellular, colonial, filamentous and multicellular 2. Composed of eukaryotic cells 3. Cell wall composed of cellulose or silicon dioxide 4. Compose phytoplankton 5. Nutrition by photosynthesis

E. Protozoa

1. Unicellular 2. Composed of eukaryotic cells 3. Animal-like 4. No cell wall 5. Nutrition by ingestion

F. Helminths 1. Multcellular 2. Eukaryotic 3. Parasitic flatworms and roundworms 4. Nutrition by parasitism by feeding off living hosts

G. Viruses 1. Acellular 2. Smaller than bacteria 3. Obligate intracellular parasites 4. Outside of the living cells, viruses cannot move, grow or reproduce 5. Inside the cell they can reproduce themselves

II. Classification A. Binomial Nomenclature System 1. Carolus Linnaeus (1735) Father of Taxonomy 2. Based on a two name system: genus and species 3. Used worldwide 4. Used for Economy, Clarity, Uniqueness, Stability 5. Capitalize first letter in genus name; italicize both words

Micrococcus luteus: micro = small; coccus = spherical; luteus = yellow Escherichia coli : Escherichia = Theodor Escherich; coli = colon Staphylococcus aureus: staphylo = cluster; coccus = spherical; aureus =

golden

B. Five Kingdom System- Robert H. Whitaker

1. Monera 2. Protista 3. Fungi 4. Plantae 5. Animalia

C. Three Domain System- Carl R. Woese

1. Bacteria 2. Archaea 3. Eukarya

D. Taxonomic Hierarchy Taxonomic Ranking Homo sapiens Escherichia coli 1. Domain Eukarya Bacteria 2. Kingdom Animalia 3. Phylum Chordata Proteobacteria 4. Class Mammalia Enterobacteriales 5. Order Primates Enterbacteriaceae 6. Family Hominidae 7. Genus Homo Escherichia 8. Species sapiens coli

III. The Discovery of Cells and Microorganisms A. Robert Hooke 1665 1. Observed microorganisms for the first time with a microscope 2. Coined the term “cell” B. Anton van Leeuwenhoek 1670’s 1. Microscope lens grinder who accidentally discovers microorganisms in a drop of water 2. Using his own microscopes, he observed sperm cells, bacteria, and red blood cells

IV. The Golden Age of Microbiology

A. Major Accomplishments

1. Louis Pasteur and Robert Koch both led the way 2. Significant developments- lasted from 1857 to 1914 (57 years) -germ theory of disease established -use of disinfectants introduced -improved surgical techniques -role of immunity established and vaccines to immunize against diseases -microbiology culture techniques

B. Spontaneous Generation

Francesco Redi- maggots come from flies

C. Louis Pasteur- Microorganisms Come from Microorganisms- Biogenesis

1. Demonstrated that microorganisms are everywhere 2. Disproved spontaneous generation of microorganisms

Swan-necked Flask Experiment

D. Fermentation Discovered (1857)

1. Pasteur was asked by the wine and beer making merchants to find out why the beverages were spoiling 2. Discovered that bacteria was contaminating vats of wine and beer which ended up with sour-tasting acetic acid (vinegar) 3. Discovered that yeast was responsible for fermentation 4. Developed the technique Pasteurization as a way to control unwanted the bacteria 5. Linked food and beverage spoilage to microorganisms 6. Considered the Father of Microbiology

E. What Causes Disease?

1. The Germ Theory of Disease -Pasteur was called upon by French merchants to determine the cause of silkworm disease -found that a protozoan was the cause of silkworm disease -for the first time a microorganism was linked to a particular disease -this ushered in the germ theory of disease 2. Pasteur developed vaccines for cholera and rabies 3. His remarkable breakthroughs in the causes and preventions of diseases 4. Edward Jenner was the first to develop a vaccine against smallpox

3. Robert Koch

-became famous for isolating Bacillus anthracis; the pathogen that causes antrax (1877); Mycobacterium tuberculosis, the tuberculosis bacillus (1882); Vibrio cholerae (1883), the causative agent of cholera, culture techniques, and for the development of Koch's postulates

-awarded the Nobel Prize in Physiology or Medicine for his tuberculosis findings in 1905 -considered one of the founders, of microbiology, along with Louis Pasteur -he inspired major figures later to come such as Paul Ehrlich and Gerhard Domagk Koch’s Postulates Isolate Incubate Infect healthy animal Identify

4. Joseph Lister was the first to use disinfectants

-he studied the disinfectant, carbolic acid (phenol) -carbolic acid had been in use as a means of deodorizing sewage -Lister sprayed carbolic acid on surgical instruments, surgical incisions

and on the dressings placed on wounds -he found that carbolic acid solution swabbed on wounds reduced the incidence of gangrene -he suggested surgeons wear clean gloves and wash their hands before and after surgery with 5% carbolic acid

F. Birth of Modern Chemotherapy: Dreams of a “Magic Bullet” 1. The “magic bullet” -treatment of disease by using chemical substances is called chemotherapy -chemotheraphy drugs are synthetic or naturally produced substance 2. Paul Ehrlich (1910) -developed salvarsanm a compound containing arsenic 606, the first

chemotherapy drug -it was the magic bullet that targeted Treponema pallidum, the microorganism that causes syphilis -awarded the Nobel Prize 3. Gerhard Paul Domagk (1930’s) -discovered protonsil, a sulfonamide drug -effective against streptococci diseases -awarded the Nobel Prize

4. Alexander Fleming (1928) -discovered the antibiotic penicillin -penicillin was isolated from the fungus, Penicillium notatum -received the Nobel Prize in Physiology or Medicine in 1945

V. Methods of Culturing and Media Classification A. Media Classification 1. Physical state of media a. liquid b. semisolid c. solid

2. Media types a. chemically defined -also called synthetic media -all the chemicals used are known

-formula known -does not contain any yeast, animal or plant tissue

b. complex media -contains a carbon source such as glucose for bacterial growth -various salts needed for bacterial growth -non synthetic -contains yeast, animal or plant tissue -formula unknown

3. Types of Media for Microbial Growth a. general purpose media -nutrient agar (NA) -nutrient broth (NB) c. selective media -selects the growth of one microorganism over another d. differential media -distinguishes one microorganism from another

-eosin-methylene blue (EMB) -selective and differential -MacConkey agar (MCK ) -selective and differential -Hektoen Enteric agar (HE) -selective and differential -manitol salt agar (MSA -selective and differential -blood agar plate (BAP) -differential -NaCl agar -selective

1. Hektoen Enteric Agar (HEK) -is a selective and differential media primarily used to recover Salmonella and Shigella from patient specimens. -contains indicators of lactose fermentation and H2S production; as well as inhibitors to prevent the growth of gram positive bacteria -Salmonella produces black colonies, whereas Shigella produces translucent green colonies, the color of the agar -sugars in media usually include lactose, sucrose, and salicin

3. Eosin Methylene Blue (EMB) -lactose fermentation produces acids, which lower the pH and encourages dye absorption by the colonies, which are now colored purple- black and display "nucleated colonies“- colonies with dark centers

-lactose non-fermenters may increase the pH by deamination of proteins which ensures that the dye is not absorbed- the colonies will be colorless -is a slightly selective stain for Gram-negative bacteria is a blend of two stains, eosin and methylene blue in the ratio of 6:1

Alpha and Beta Hemolysis Gamma Hemolysis

B. Comparative Sizes of Microorganisms

VII. Microscopy

A. Factors Affecting Microscopy

1. Magnification 2. Resolution

B. Brightfield Microscope

1. Microscope parts 2. Lens system

-the refractive index is the light-bending ability of a medium-the light may bend in air so much that it misses the small high-magnification lens-immersion oil is used to keep light from refracting

C. Darkfield Microscope

D. Phase Contrast microscope

E. Electron Microscope

SEM (scanning electron microscope) TEM (transmission electron microscope)

F. Preparing Smears for Staining

1. Smear preparation 2. Heat fixing 3. Staining -stains are salts composed of positive or negative ions -basic dyes attracted to slightly negative bacteria stains bacteria crystal violet, methylene blue, malachite green, safranin -acidic dyes negative stain does not stain bacteria nigrosin, India ink, eosin

G. Simple Staining 1. Used to highlight microorganisms 2. Mordants are sometimes used to intensify stain

H. Differential Staining 1. Gram stain crystal violet, mordant, decolorizer, safranin

2. Acid-fast stain carbolfuschin, decolorizer, methylene blue

3. Endospore stain malachite green, safranin

I. Special Staining 1. Capsule stain 2. Flagella stain