Lecture 1

-Microbes in the news: Yersinia pestis and Bubonic Plague, Legionella pneumophila and Legionnaire’s Disease. Pseudogymnoascus destructans and White-nose Syndrome/ WNS, Ebola virus and Ebola vaccine

-what are “pathogens”? pathos=suffering

-why are some of the pathogens’ names italicized and others are not?

-Why do we care about microbiology?

Why is teamwork important in microbiology?

-Ebola outbreak, work to control, work to develop Ebola vaccine

-Why is micro history of importance? (Bubonic Plague and Ebola)

-other Micro topics “ in the news”:

-microbes and climate change (see paper/Ppt on D2L site)

-Human microbiome and influence on human health,

- Harmful Algal Blooms/ HAB’s along Pacific coast, Alexandrium/Pseudonitzschia species, neurotoxin domoic acid and Amnesic Shellfish Poisoning/ASP (update: cyanobacteria and toxins in freshwater Russian River, Sonoma County, CA 8.2015)

-What is microbiology? The study of microbes/microorganisms

I. Microorganisms: (Gr. mikros, small) organisms too small to be seen with the naked eye

Microbes = <~100-200 µm

-resolving power of human eye without magnifying device ( the “naked eye”) ~200 µm

- what is “µm” ? micrometer= µm = 10^-6 m

2. Evolution of microbes

Bya= billion years ago What is a billion? billion= 10⁹

~4.6-4.8 bya Earth forms

~3.6-3.8 bya first cells evolve LUCA= Last Universal Common Ancestor

-LUCA= single cell, no nucleus = prokaryote

-Earth’s atmosphere= no free molecular oxygen, O₂ = anoxic/anaerobic

-Biological evolution: the change in the genetic make-up of a population of organisms over time

-One mechanism by which biological evolution may occur is “natural selection” roughly described = those variants in a population of organisms best adapted to a specific environment will survive and reproduce and pass on their genetic information at higher rates than those variants less adapted to a specific environment (drives biological evolution)

~2.5 bya cyanobacteria and oxygenic photosynthesis evolve, Earth atmosphere slowly

accumulates O₂ (O2 is toxic to most cells at this time unless living in anaerobic environments for e.g. sea bottoms). Through endosymbiosis, a primitive nucleated phagocytic cell may have phagocytized a primitive bacterium which evolved into a “peroxisome”, detoxifying toxic hydrogen peroxide made in an aerobic environment... Subsequent endocytosis of aerobic respiring bacteria may have led to evolution of eukaryotic mitochondria.

~ 2 bya evolution of eukaroytes as described above

~2 bya eukarotes evolve ( have a membrane bound nucleus and other membrane organelles such as mitochondria, chloroplasts)

~ 1.3 bya algal diversity

~ 1.2 bya sexual reporduciton evolves

~1 bya multicellular animals evolve

~600 mya early animals sponges evolve

~2.8 Homo appears in East Afric

~ 2.3 mya early human ancestor Homo habilis evolves

~200-250 kya earliest Homo sapiens?

A. Distinguish cellular microbes (example bacteria) vs acellular “agents” (examples viruses, prions)

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Acellular microbial agents Cellular microorganisms

prions viruses prokaryotes eukaryotes

spongiform encephalopathies HIV Bacteria: Protozoa:

“Mad Cow Disease” Ebola Mycobacterium tuberculosis/TB Plasmodium/malaria

Kuru Hanta Staphylococcus Cryptosporidium

Creutzfeldt-Jakobs Disease Polio Bacillus anthracis/anthrax Giardia

Chronic Wasting Disease Rabies E. coli Trypanosoma/sleeping sickness

Hepatitis Salmonella

Smallpox Chlamydia/STD Fungi:

Treponema pallidum/syphilis Candida/yeast

Coccidioides

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Family Trees of Cellular Life based on rRNA sequences by Carl Woese

Acellular microbes:

Do not synthesize cell membranes

Prions: misfolded cellular proteins, no nucleic acid/gentic info. “BSE, Mad Cow

Disease, Kuru

Viruses: nucleic acid wrapped in protein, obligate intracellular parasites

Cellular Microbes: 3 Domains

Prokaryotes lack a nucleus= Domain Bacteria and Domain Archaea

Eukaryotes have a nucleus and other membrane bound organelles such as

mitochondria, chloroplasts= Domain Eukarya

Prokaryotes

1. Domain Bacteria: unicellular, most have cell walls containing peptidoglycan

2. Domain Archae: lack peptidoglhycan, methanogens, extremophiles such as

thermophiles and halophiles

Eukaryotes Domain Eukarya

- divided into “Kingldoms:

-(outdated Kingdom Protista: e.g. protozoa, algae)

Kingdom Fungi: yeast, mold, fleshy fungi

-Kingdom Plantae: e.g. Elodea in lab

-Kingdom Animalia: parasitic worms/helminths, arthropod vectors, human hosts

- Processes associated with microorganisms-all associated with microbes search for and acquisition of energy and building blocks for growth and reproduction
A. Decomposition (recyclers), fermentation (preservation), pathogenesis (cause diseases by toxin production/interrupting normal host homeostasis), production of beneficial compounds (ex. antibiotics, vitamins), geochemical agents (nitrogen, carbon, sulfur cycles), bioremediation (breakdown, detoxify compounds in environement).

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-. Microbes receive a lot of “bad press” as causes of infectious diseases but there are many more “good” microbes than “bad” microbes.

Microbes could easily survive without humans, other animals and plants; humans, other animals and plants could NOT survive without microorganisms.

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“Cast of Characters” details

Microbes

I. Acellular Agents

A. Viruses: NOT cells; subcellular metabolic parasites; single- or double stranded DNA or RNA; protein coats/capsids; +/- envelope derived from host cell membrane; ex influenza, vaccinia, small pox, polio, Ebola, hanta virus, Human Immunodeficiency Virus HIV

B. Prions: proteinaceous infectious particles. Infectious agents made only of protein (hypothesis).

Cause spongiform encephalapathies such as Kuru, Mad Cow Disease, Creutzfeldt-Jakobs Disease

II. Cellular Microorganisms

A. Prokaryotic microorganisms (L, Gr pro, before; Gr karyo, nut or nucleus) organisms lacking a membrane-bound nucleus and other membrane bound organelles. Unicellular.

1. Domain Archaea: (archaea pl. /archaeon sing.) primitive anaerobes, found in extreme environments ex. methanogens, halophiles, thermophiles (no known pathogens)

2. Domain Bacteria (bacteria pl./ bacterium sing.)

a. Cyanobacteria : photosynthetic with generation of oxygen; autotrophs therefore do not need to invade other organisms; variable habitats; some fix nitrogen; some toxin producers

b. Gram-positive bacteria: saprophytes, pathogens: ex Streptococcus, Staphylococcus, Clostridium, Bacillus, Corynebacterium

c. Gram-negative bacteria: ex “enterics”= Escherichia coli E. coli, Salmonella, Shigella, Yersinia; others= Neisseria gonorrhoeae/gonorrhea, Legionella, Brucella, Bordetella pertussis/whooping cough

d. Mycoplasma: very small, lack cell wall, sterol in cell membrane, saprophytes, human and animal pathogens ex Mycoplasma pneumoniae

e. Spirochetes/Spirillla: helical, motile, outer sheaths, axial filaments: sewage, mud, mouth, genitals. pathogens= Treponema pallidum=syphilis

Borrelia burgdorferi=Lyme Disease

f. obligate intracellular parasites

i. Rickettsia: enzyme deficiencies; many transmitted by arthropod vectors. Rickettsia typhi= endemic typhus; R. rickettsia=Rocky Mountain Spotted Fever

ii. Chlamydia: Chlamydia psittaci=ornithosis; C. trachomatis= STD, sterility, conjunctivitis, infant pneumoniae

B. Eukaryotic Microorganisms (Gr eu, well, good, true) organisms containing membrane-bound nucleus. Unicellular, colonial, or multicellular.

1. Domain Eukarya

a.Protista:i. protozoa:unicellular ex Plasmodium=malaria, Giardia, Entamoeba

ii. plantlike: algae, euglenoids, diatoms, dinoflagellates:oxygenic photosynthetic; major CO2 fixers; chlorophyll a; some toxin producers. Phytoplankton, diatoms, dinoflagellates Gymnodinium, Gonyaulax produce red pigment and neuortoxin= ”red tides”

b. Fungi: unicellular yeast=Candida, Saccharomyces; multicellular Penicillium, Trichophyton, Coccidioides, Aspergillus

Brief History of Microbiology I. Era of Speculation: 5000 BCE-1675 CE

-. Era of Observation: approx 1675-1850’s

A. Development of Microscopy

1. Robert Hooke;coins term “cell”

2. Anton van Leeuwenhoek 1632-1723; first to observe and report existence of microbes/ “animalcules”

B. Disproof of Spontaneous Generation Theory

1. Francesco Redi-1660

(2. Lazzaro Spallanzani-1760)

3. Louis Pasteur-1861

4. John Tyndal

C. Early medical advances

1. Edward Jenner: 1798 smallpox vaccine

2. Ignaz Semmelweiss-1840 need to wash hands after performing autopsies and before performing exam on patients

III. Era of cultivation (Golden Age of Microbiology) 1850-1890

A. Louis Pasteur

1. spontaneous generation (swan-neck flasks) 1859

2. distribution of microbes in air

3. fermentation

4. pasteurization

5. vaccines (chicken cholera/rabies)

6. laid foundation for germ theory of disease

B. Joseph Lister (1860’s-70’s): antisepsis , carbolic acid during surgery, wounds, bandages

C. Germ Theory of Disease

D. Robert Koch (1870’s)-”one disease-one organism”

1. pure culture technique

2. agar (red algae Gelidium/Gracilaria, w. Pacific Ocean); petri dish/agar plate 3. Koch’s postulates

4. anthrax (Bacillus anthracis), tuberculosis (Mycobacterium tuberculosis), cholera (Vibrio cholera)

IV. Immunology

A. Elie Metchnikoff- 1880’s phagocytes

V. Virology

A. Dimitri Iwanowski-1892: provides evidence for virus causation of Tobacco Mosaic Dz.

B. Electron Microscope: Germany; US. approx 1939

VI. Chemotherapy

A. Paul Ehrlich-1910: chemotherapeutic agent for syphilis; “salvarsan”

B. Alexander Fleming-1928; discovers penicillin

C. Gerhard Domagk-1935: discovers prontosil (sulfa drugs) inhibits bacteria

VII. Microbes as geochemical agents

A. Sergius Winogradsky and Martinus Beijerinck-1887-1890

1. Carbon, nitrogen and sulfur cycles

2. enrichment culture