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Chapter 1 The Science of Microbiology

BIO 2924
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Ancient history!

Bacteria Put the first molecular oxygen in the earths atmosphere, creating the ozone layer that protected Earths surface from killing radiation. Created conditions permitting the later evolution of oxygen-utilizing creatures such as us. Have a varied metabolic capabilities that allowed them to survive under an impressive variety of conditions.

Never Underestimate the Power of Bacteria

They learnt to maximize modify their genome (DNA) thereby creating new capabilities that enabled them to colonize many niches on Earth. No part of Earth has been found free of bacteria from the arctic ice to the deep subsurface of land masses, from the depths of oceans to boiling hot springs. They are specialists in metabolic diversity. Eukaryotes generally expand their metabolic diversity by acquiring bacteria or archaea as ENDOSYMBIONTS

Recruiting Endosymbionts

Plants acquired photosynthetic bacteria that later modified into chloroplasts. Root nodules of legumes have bacteria that can fix atmospheric nitrogen, making the plant self-fertilizing. Animals recruited bacteria and archaea to colonize their intestinal tracts for protective or nutritional reasons. Ruminants (e.g., cattle, goats) rely on ruminal bacteria to digest grasses and other forages. No single bacterial species that is essential to man. - Picture of the Bubble Boy Page 483


PROKARYOTES 01-10.jpg figure

Formerly known as Archaebacteria


Bacteria and archaea were the first life forms to appear, about 3.5 4 billion years ago, and ruled undisputed for a billion years before the first eukaryotes appeared on ancient earth.

The Scope of Microbiology Seven divisions of Classification 1. Bacteria: Prokaryotic 2. Archaea: Prokaryotic 3. Algae: Eukaryotic 4. Fungi: Eukaryotic 5. Protozoa: Eukaryotic 6. Viruses: Acellular 7. Helminths: Eukaryotic Prokaryotic: before a nucleus Eukaryotic: true nucleus

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The study of Microorganisms (microbes) Cannot be seen by the unaided eye Prokaryotes Before a nucleus lack a nucleus Eukaryotes After a nucleus blessed with a nucleus!

7 divisions of Classification
1. Eubacteria (Modern Prokaryotes)

1/1000th the size of a eukaryotic cell Mostly unicellular Different shapes and sizes Can grow at varied temperatures (-20oC to 110oC) Can withstand extremely acidic to alkaline conditions Autotrophs, decomposers Vast spectrum of diseases important uses

2. Archaea (Ancient Prokaryotes)

7 divisions of Classification

Initially Archaebacteria Hostile environments, Extreme heat, high acidity, high alkalinity, high salt concentration E.g., Methanogens (not human pathogens) plant-like, photosynthesis Unicellular microscopic to multicellular macroscopic Critical to global ecology, negligible medical importance Nonphotosynthetic, mostly multicellular Mostly scavengers, decompose dead organisms Mostly responsible for plant diseases Corn smut, wheat rust economically important Some human diseases Pneumocystic pneumonia in AIDS patients (Pneumocystis carinii), Hallucinations (Amanita)

3. Cyanobacteria (Prokaryotic) & Algae (Eukaryotic)

4. Fungi (Eukaryotic)

5. Protozoa (unicellular) parasitic diseases

7 divisions of Classification

motile, animal like, complex architecture E.g., amoeba, flagellates, ciliates malaria, sleeping sickness: Parasitic diseases DNA or RNA wrapped up in a protein coat 1/1000th 1/10th size of bacteria: Electron Microscope E.g., virions, prions etc Cannot reproduce outside of host cell. Cause of smallpox, yellow fever, polio, AIDS, common cold, flu, ebola, etc PRION: scrapie (sheep), mad cow disease, CJD (human) Worms macroscopic, microscopic. Belong to the animal kingdom Flatworms (beef tapeworm, liver trematodes) Roundworms (hookworms, trichinella)

6. Viruses (plant, animal or bacterial) - Acellular

7. Helminths (multicellular) Parasitic diseases

A Brief History of Microbiology

Bubonic Plague or Black Death: 25 million casualties in the Europes Middle ages (1347 lasted 20 years) Causative organism Yersinia pestis (Y. pestis) Yersinia infested fleas, whose hosts were rats. Rats died, and the bacterium spread to humans. Disease causes subcutaneous hemorrhaging, and spots of blood which turn black, to accumulate under the skin Buboes swollen lymph nodes Buboes often become open sores Can also affect the lungs pneumonic plague Still found among squirrels in parts of the U.S.
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Buboes in Fig 1 & 2: Swollen lymph nodes

Fig 1 Fig 2

Black spots formed due to hemorrhaging

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A Brief History of Microbiology

Childbed fever (Puerperal fever) (Mid 1800s) Caused by the bacterium Streptococcus pyogenes Symptoms: fever, chills, delirium and death In the past centuries, it was the greatest killer of women. One sixth of women died of this fever Caused by infection of the genital tract shortly after giving birth (latin puer child). Any fever within 2 weeks of childbirth is dangerous since it can cause infertility and septicemia ( presence of infectious microbes in the bloodstream, causing sepsis) Ignaz Semmelweis showed that sanitary techniques virtually eliminated puerperal fever in hospitals. He used chlorine as a disinfectant He was treated with skepticism and ridicule

A Brief History of Microbiology

The Great Irish Famine (1845 1849) Potato blight that led to the death of >106 people caused by the potato fungus or Phytopthora infestans Potatoes infected with late blight are shrunken on the outside, corky and rotted inside

Photo by Scott Bauer.

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Brief History of Microbiology

1674 1796 1847 1859 1865 1876 1892 1894 1929 1977 1982 1983

Leeuwenhoek: sees microorganisms Jenner: vaccine for smallpox Semmelweiss: cause of childbed fever Pasteur: disproves spontaneous gen. Lister: introduces antiseptic technique Koch: pure culture on agar/Postulates Iwanowski: discovers viruses Ehrlich: selective toxicity (Salvarsan) Fleming: discovers penicillin Woese: classifies Archaea Stanley Prusiner discovers prions Luc Montaigner , HIV/AIDS
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Robert Hooke - 1665 Coined the word cell after Looking at cork slices Schleiden & Schwann - Came up with the Cell theory - cell is the basic unit of living beings - All cells arise from preexisting cells Anton Von Leeuwenhoeks Animalcules 1674 A draper with very little schooling. Later he was appointed janitor at the Delft City Hall in Holland. Best lens maker of his time! His hobby was making little glass lenses. Peter the Great paid his respects. He was the first to see blood moving thru capillaries In 1680, was elected a Fellow of the Royal Society. Kept detailed notes and sketches. Published over 400 scientific papers. Ground 419 lenses in his life.

Advances in Microbiology

Advances in the Germ Theory of Disease

Ignaz Semmelweis 1847 Physician in obstretrics ward of a Vienna hospital Maternity patients contracted blood-poisoning from doctors who also handled corpses at the morgue and didnt wash their hands before handling maternity patients Proved that hand washing with Chlorine cut down the mortality rate of childbed fever His doctrine was dismissed by most doctors! Interestingly The same bacterium also causes scarlet fever

The Middle Ages: Microbiologys Dark Age!

Transition period: Microbiology had no focus during this period, several flawed theories held sway! Miasmatic theory of disease: Diseases such as cholera and the black plague were caused by a miasma (Greek, pollution), or bad air. Cholera was believed to be spread through air, because it was epidemic in places where the water was stagnant and foul smelling. Theory of Spontaneous Generation (Abiogenesis) The belief: complex living organisms arise spontaneously from decaying organic substances Eg: maggots spontaneously appear in meat, mice from dirty hay, and fleas from putrid matter.

Microbiology Dark Ages!

John Needham (British Clergyman) did experiments with meat broth that he felt supported spontaneous generation. Francesco Redi proved that no maggots appeared in meat when flies were prevented from laying eggs Spallanzani showed that microbes came from air, and could be killed by boiling meat broth that is boiled in a sterile environment stays uncontaminated Despite these great experiments, the supporters of spontaneous generation were not convinced.
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Spontaneous Generation Proven Wrong

Louis Pasteur (French Scientist) 1822 - 1895 Also known as the Father of Microbiology Ushered in the golden age of Microbiology, with 2 important areas of research: Definitively disproved Spontaneous Generation by his famous Swan Necked Flask Experiment Invented the Germ Theory of disease germs, and not bad air cause disease Best known for showing how to stop milk and wine from going sour Pasteurization Created the first vaccine for rabies

Louis Pasteur and the Germ Theory

Pasteur demonstrated that fermentation is caused by the growth of microbes in nutrient broth, and the growth of microbes in nutrient broths is not due to spontaneous generation. He exposed boiled broths to air in vessels where air was admitted via a long tortuous tube that would not allow dust particles to pass because of its shape and thinness. Nothing grew in those broths. The living organisms that grew in those broths came from outside, as spores on dust, rather than by spontaneous generation.
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The Swan Flask made by Pasteur

All the germs (spores etc) settle here and dont enter the flask The broth, that has been boiled in this flask, stays uncontaminated. It will get contaminated only if the flask is tilted and the liquid allowed to come in contact with the spores that have settled in the region shown above

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Swan Necked Flask Experiment

Boiled meat in a Swan necked flask that allowed air but not microorganisms Proved that microorganisms causes the broth to spoil.

Disproved Spontaneous Generation Fermentation Silkworm disease Pasteurization Developed vaccines Chicken cholera Louis Pasteur 1822 1895 Anthrax Rabies

Stimulation of the bodys defense mechanism to combat and ward off infection. Edward Jenner- 1749-1823 Observed that the dairymaids who naturally contracted a mild infection of cowpox were immune to smallpox Inoculated fluid from cowpox blisters from a dairymaid into an 8 year old boy (James Phipps) of a local farmer. The boy contracted cowpox. The boy was inoculated with fluid from a smallpox blister. Showed no signs of smallpox (immunity!) Vaccination (latin vacca = cow) The Turkish inoculation practice: Circassian method of inoculation had been followed for centuries Lady Mary Montagus letters


Cause and Effect in Infectious Disease Research

By 1800s: Microbiologists struggled to identify microbes that cause diseases like Cholera and TB Disease can be caused by microbes too small to be seen? Yeah right! Robert Koch 1876 Infectious disease research needs a rigorous scientific basis. Proposed 4 criteria for establishing a cause and effect relationship between microbe and disease - KOCHS POSTULATES Used agar to obtain pure cultures of microbes

Developed techniques for culturing bacteria in the laboratory Developed steam sterilization Etiology of anthrax, cholera, tuberculosis, sleeping sickness Kochs postulates Robert Koch 1843 1910
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I know what youre up to!: Cause and Effect

Robert Koch (German Scientist) 1. Isolated anthrax bacillus from dead cows 2. Cultured them in nutrient broth 3. Intentionally injected the cultured bacilli into mice. Mice died. 4. Isolated and cultured anthrax bacilli from dead mice tissues. Also famous for developing pure culture techniques for isolating and growing bacteria Used agar for the first time to grow colonies (clones) of bacteria on solid media Obtained the agar from his neighbours pantry

1. Microbe must be associated with disease-lesions found in diseased but not healthy tissue 2. Microbe must be isolated from disease-lesions as a pure culture 3. Pure culture of the microbe should cause disease symptoms if inoculated into humans or animals 4. Microbe must be re-isolated in pure culture from humans or animals used to satisfy the 3rd postulate. Invaluable for proving that a specific disease is caused by a particular microbe 5. Led to the isolation of almost all bacterial diseases prevalent in Europe (typhus, dysentery, syphilis, gonorrhea, pneumonia etc) 1. Koch himself identified the rod shaped bacterium Mycobacterium tuberculosis that causes TB.

Sir Joseph Lister (British Surgeon) Aseptic technique - Surgery mortality from 70% - 15%. - Use of Phenol as a disinfectant. Alexander Flemming The first chemotherapeutic agent, Penicillin. Antibiotics: produced by microbes Paul Ehrlich Stained the bacterium of tuberculosis Discovered the dye Trypan Red that destroyed trypanosomes heralded the era of chemotherapy

Preventing Microbial Attack!

Microbiology in the Modern Era

Paul Erlich: Selective toxicity. Salvarsan was used to treat syphilis Sulfa drugs (first chemotherapeutic drugs) WW1 Antibiotics Widespread clinical use was in1950s Immunology Virology Iwanowsky discovered TMV Viruses much smaller than bacteria. Seen via EM Filtration can separate viruses from bacteria Genetic Engineering Cloning: insulin production in E. coli Environmental Microbiology: Bioremediation (cleaning up the environment using microbes that degrade toxic chemicals)

Emerging and Re-emerging Infectious Diseases The first cracks in the protective shield against microbes began to appear in the 1980s. Old standbys like penicillin were no longer fully protective. By 1995, infectious diseases became one of the top five causes of death in the United States Disease patterns change Bacteria change Human activities change creating new opportunities for bacteria to cause disease Foodborne and waterborne illnesses Nosocomial infections Bioterrorism Antibiotic resistance

Submerging Infectious Diseases

Waning bacterial diseases Syphilis FIELDS IN MICROBIOLOGY Medical microbiology Environmental microbiology Industrial microbiology Agricultural microbiology Look up Table 1.1 (important)

Disease Category New-new

Definition New diseases caused by newly discovered bacteria Diseases caused by newly recognized pathogens that have been around for long Old diseases that have reappeared Long-known pathogens acquiring traits that make them more dangerous


Lyme disease Legionnaires disease


Campylobacter foodborne disease


TB, Cholera, Diphtheria

Antibiotic resistant bacteria


Old diseases with known causes being recognized now

C. trachomatis gonorrhea

Some Examples of Bacterial Shapes



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Growth on an Agar Containing Petri Dish

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Opalescent Pool in Yellowstone National Park, Wyoming USA. K. Todar. Conditions for life in this environment are similar to Earth over 2 billion years ago. In these types of hot springs, the orange, yellow and brown colors are due to pigmented photosynthetic bacteria which make up the microbial mats. The mats are literally teeming with bacteria. Some of these bacteria such as Synechococcus conduct oxygenic photosynthesis, while others such as Chloroflexus conduct anoxygenic photosynthesis. Other non-photosynthetic bacteria, as well as thermophilic and acidophilic Archaea, are also residents of the hot spring Raven - Johnson - Biology: 6th Ed. - All Rights Reserved - McGraw Hill Companies community.