Chapter 1 Objectives:

• What is Microbiology?
• Learn the origins of Microorganisms & their roles in the earth's environment
• Learn how humans use Microorganisms
• Learn about Infectious Disease and it's impact on humans
• What are the general characteristics of Microorganisms
• Historical foundations of Microbiology
• Taxonomy: Organizing, Classifying, and Naming Microorganisms
  

What is microbiology?
Microbiology is a specialized area of biology that deals with living things ordinarily too small to be seen without magnification (microscopic). Microbiology is one of the largest and most complex of the biological sciences because it integrates subject matter from many diverse disciplines.

Specialty Professions of Microbiology

• Geo-microbiologists-- focus on the roles of microbes in the development of earth's crust.
• Marine Microbiologists-- study the oceans and its smallest inhabitants.
• Pharmaceutical Microbiologists-- discover and develop new drugs from microbial sources.
• Nurse Epidemiologists-- analyze the occurrence of infectious diseases in hospitals.
• Astrobiologists-- study the possibilities of organisms in space.

Bacteria
-single cell microorganisms
-very diverse
-can live independently
-procaryotes (no nucleus or organelles)
-have been on earth for at least 3.5 billion years
-eucaryotes-have a nucleus and organelles
-includes both true bacteria and archaea
-they are adaptive (can adjust to different environments)
-Archaea are really quite different than bacteria but for our purposes we lump them together (they are both prokaryotes at least!). You can join an expedition looking for extremophiles in a Russian Hotsprings!

Viruses

-They don't know how to classify them
-not alive
-they need a living cell to multiply

Fungi
-they are eukaryote
-their spores are microscopic
-molds fall into this category
-antibiotics are made from different molds

Protozoa
-"before animals"
-they are eukaryote
-very complex single celled organisms (some have the most complex cells you will see)
-very diverse
-most are not parasitic
Here is a video of looking through a microscope at a drop of pond water that is full of paramecia (a type of protozoan). You will see they swim very quickly, and that they can draw material quickly into their cell. Part of the video is low-power magnification, and part of it is higher power.

Can be problematic if you have a weakened immune system.
Lack of round worms may contribute to allergies and autoimmune diseases.



Helminths
-multicellular worms
-we can see them sometimes
-microscopic eggs
-their make up is very similar to humans, that is why they are so hard to treat once they have infected humans.
What kills them can kill us too.





Lifestyles of microorganisms
-Free-living
*Auto-trophic-A microorganism that requires only inorganic nutrients and whole source of carbon is carbon dioxide.
-Hetero-trophic
*An organism that relies on organic compounds for its carbon and energy needs.
-Parasitic
*Very few cause disease in humans
*The ability of viruses to infect bacteria maybe a new tool in the arsenal against pathogens.


The Scope of Microbiology

• Epidemiology - Study of incidence, distribution and control of disease in population. (Center for Disease Control) Includes the study of factors affecting the progress of an illness, and in the case of many chronic diseases, their natural history. With this careful monitoring, they can help to prevent major breakouts of disease. They have the power to quarantine any suspect people or groups if necessary.
• Biotechnology - The industrial application of living organisms and/or biological techniques developed through basic research. Biotechnology products include pharmaceutical compounds and research materials, fermentation to make wine, Pasteurization, penicillin, insulin, cloning, gene therapy, etc. This process includes any process in which humans use metabolism of living thinks to arrive at a desired product, ranging from bread making to gene therapy.
• Bioremediation- A natural process in which environmental problems are solved by the use of bacteria or other microorganisms that break down a problem substance, such as oil, into harmless molecules
• Immunology- studies the complex web of protective substances and cells produced in response to infection. Including areas such as vaccination, blood testing and allergy. It also concerns itself with the study of hypersensitivity; inappropriate immune responses that can be harmful to the human host. Allergy is an example of hypersensitivity.
• Food, Dairy, and Aquatic Microbiology- Examine the ecological and practical roles of microbes in food and water.
• Genetic Engineering- Deliberately altering the genetic make-up of microbes, plants and animals for the purpose of creating new substances and genetically modified organisms.

In the news: Biotechnology is a booming business!!

Impact of Microbes on Earth

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Microbes are very ubiquitous (being or seeming to be everywhere at the same time). Microbes can be found nearly everywhere, from deep in the earth's crust, to the polar ice caps and the ocean, to the bodies of plants and animals. Even though they are mostly invisible they make up for their small size by occurring in larges numbers and living in places that many other organisms cannot survive. Above all, they play central roles in the earth's landscape that are essential to life.

• Procaryotes appeared about 3.5 billion years ago and were alone on the earth for about 1.5 billion years.

(eukaryote-more complex type of cell- that has a nucleus-appeared about 1.9 billion years ago. Eu-cary means true nucleus, it tells you that the first inhabitants lacked a true nucleus which is what pro-cary means pre-nucleus.)

• Microbes are involved in: nutrient production, energy flow, decomposition, production of food, drugs and vaccines, bioremediation, causing disease.
• Photosynthetic microorganisms, including algae, account for more than 50% of the earth's photosynthesis, contributing the majority of the oxygen to the atmosphere
• Other microbes are responsible for the breakdown and recycling of nutrients through decomposition. Microbes are essential to the maintenance of the air, soil, and water.
• Human use of microorganisms- microbes have been called upon to solve environmental, agricultural, and medical problems.
• Biotechnology applies the power of microbes toward the manufacture of industrial products, food, and drugs.
• Microbes from the basis of genetic engineering and recombinant DNA technology, which alter genetic material to produce new products and modified life forms.
• With bioremediation, microbes to clean up pollutants and waste in natural environments.
• Impact of pathogens
  Nearly 2000 different microbes are pathogens that cause infectious diseases. Many older disease are also increasing.
  10 billion infections/ year worldwide
  13 million deaths from infections/year worldwide
  Many diseases previously considered noninfectious are now known to be linked to microbes.

Human Use of Microorganisms
Yeasts, a type of microscopic fungi, cause bread to rise and ferment sugar to alcoholic beverages. Historical records show that households in ancient Egypt kept moldy loaves of bread to apply directly to wounds and lesions, which was probably the first use of penicillin.
-Genetic engineering is a newer area of biotechnology that manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms.
-recombinant DNA has made it possible to deliberately alter DNA and switch genetic material from one organism to another.Bacteria and Fungi were some fo the first organisms to be genetically engineered, because they are so adaptable to changes in their genetic makeup. This technology has unlimited potential in terms of medical, industrial, and agricultural uses.Microbes can be engineered to synthesize desirable proteins such as drugs, hormones, and enzymes.




Infectious Diseases and the Human Condition

-An increase in people with a weakened immune system is contributing to an increase in morbidity (contracting infectious diseases/illness). They are also more severely affected by minor infections which increase mortality rates.
-There are many new pathogens (microbes that cause infection) emerging every day.
-Several "old" pathogens are mutating into super-bugs that are resistant to traditional treatments and medications.
-Previous noninfectious diseases are suspected to involve microbial infections.
- Malaria, which kills more than a million people every year worldwide, is caused by a microorganism transmitted by mosquitoes. The most effective way to prevent infection is to use nets over beds because mosquitoes are most active in the evening. However, this precaution is often too expensive for some.
From the standpoint of infectious diseases, the earth's inhabitants serve as a collective incubator for old and new diseases, we are seeing SARS, AIDS, hepatitis C, and viral encephalitis as a few of some examples of recently identified diseases that cause sever mortality and morbidity and a re currently on the rise.
-Multiple sclerosis, obsessive compulsive disorder, and coronary artery disease have been linked to chronic infections with microorganisms.
-Helicobacter is a bacteria that causes stomach ulcers.
-Helicobacter pylori (H. pylori) is a bacteria that weakens the coating of the stomach and the duodenum causing digestive juices to irritate the sensitive lining of these organs. H. pylori causes stomach ulcers and also chronic gastritis(inflammation of the stomach).
Worldwide mortality due to infectious diseases[6] Rank Cause of death Deaths 2002 Percentage of
all deaths Deaths 1993 1993 Rank

General Characteristics of Microbes
Although some microbes are deadly, most are harmless, and some are extremely beneficial. These microscopic organisms can be found virtually anywhere- in air, water, plants, animals, and humans.

1. Cellular organization: (Excluding viruses there are two types of microorganisms)
a. Prokaryotes-small and lack a nucleus, organelles, and histones. However, even though they lack a nucleus, they still have DNA.
b. Eukaryote-Larger and have both a nucleus, organelles and histones.
2. Viruses
a. Viruses are not cellular and therefore sometimes called particles rather than organisms. They are included in microbiology because of their small size and close relationship with the cell.
b.Viruses are much simpler than cells; they are composed essentially of a small amount of hereditary material wrapped up in a protein covering.
c.some biologists refer to viruses as parasitic particles; others consider them to be very primitive organisms.

3. Microbial Dimensions: How small is small?
a. Microbes are too small to see with the unaided eye.
b. Microorganisms are measured in micrometers with two exceptions. The helminths are measured in millimeters, and the viruses are measured in nanometers. (fig. 1.7 pg. 8)

4. Lifestyles of microorganisms
a. Most microorganisms are harmless, free-living species that perform vital functions in both the environment and larger organisms. Few species are agents of disease.

Historical Foundations of Microbiology
Ancient cultures and civilizations had no idea that microbes existed but they did comprehend some of their important effects. For example:

• Ancient Egyptians were among the earliest people to use fermentation to brew their own beer and bread.
• The Romans liked to have good sanitation and prized clean drinking water.
• Ancient Chinese immunized people against smallpox by having them inhale dried, powdered scabs from those suffering from a mild form of the disease.
• Many traditional cultures have also recognized and used plants as remedies for certain diseases. For example, South Americans recognized the usefulness of extracts Cinchona tree (containing quinine) to treat malaria. The importance of traditional healers is being re-discovered by the West and has contributed to the field of ethnobotany.
• Many cultures recognized the communicability of certain diseases. Unfortunately, this recognition led to fear of and discrimination against sick people. These fears still persist today.
• Ignaz Semmelweis– Vienna hospital 1847. High mortality of childbirth fever. After dissecting cadavers they would go deliver babies and would cause transfer of germs. He was treated with skepticism for coming up with hand washing.
• Joseph Lister – started the trend of aseptic techniques.
• Robert Koch and Germ Theory of Disease –established a sequence of experimental steps to show that a specific m.o. causes a particular disease. Developed pure culture methods and identified cause of anthrax, TB and cholera.
• Leeuwenhoek discovered organisms (animalcules) with his simple microscope. Establishment of the scientific method-Form a hypothesis-a tentative explanation that can be observed and experimentation. A lengthy process of experimentation, analysis and testing either supports or refutes the hypothesis. Results must be published and repeated by other investigators. If hypothesis is supported by a growing body of evidence and services rigorous scrutiny, it moves to the next level of confidence-it becomes a theory. Evidence of a theory is so compelling that the next level of confidence is reached-it becomes a Law or Principle.
• Spontaneous Generation-Early belief that some form of life could arise from vital forces present in non-living or decomposing matter.
• John Needham-put boiled nutrient broth into a covered flask.
• Louis Pasteur-Showed microbes caused fermentation and spoilage. Disapproved spontaneous generation of M.O., developed aseptic techniques. Developed a rabies vaccine. In 1864 he created pasteurization.
• Germ theory of disease-Many diseases are caused by the growth of microbes in the body and not by sins, bad character, or poverty, etc.
• Alexander Fleming- In 1929 he began using penicillin to treat sickness.
• Insulin- In 1978 insulin started to be made from pigs.

Taxonomy: Organizing, classifying, and naming microorganisms

The hierarchical scheme for classification, identification, and nomenclature (a set system for scientifically naming organisms, enzymes, anatomical structures, etc.) for organisms is called Taxonomy. Below shows each category (taxa) ranging from general or broad down to specific.

Classification-The orderly arrangement of organisms into groups, showing evolutionary relationship.

Nomenclature-the process of assigning names to the various taxonomic rankings of each microbial species.

Identification-the process of discovering and recording the traits of organisms so that they may be placed in an overall taxonomic scheme.

Kingdom - king
Phylum - Phillip
Class - comes
Order - over
Family - for
Genus - great
Species - sex
(or if you are a modest sort, King Philip Comes Over For Goose Soup!)

Kingdom: Animalia, Protista, Includes Protozoa and algae
Phylum: Chordata, Ciliophora, Only Protozoa with cilia
Class: Mammalia, Hymenostomea, Single cells with regular rows of cilia; rapid swimmers
Order: Primates, Hymenostomatida, Elongate oval cells with cilia in the oral cavity
Family: Hominoidea, Parameciidae, Cells rotate while swimming and have oral grooves
Genus: Homo, Paramecium, Pointed, cigar-shaped cells with macronuclei and micronuclei
Species: Sapiens, Caudatum, Cells cylindrical, long, and pointed at one end.





Evolution-living things change gradually over millions of years
-Changes favoring survival are retained and less beneficial changes are lost.
-All new species originate from preexisting species.
-Closely related organism have similar features because they evolved from common ancestral forms.
-modern taxonomy based on DNA analysis and phylogenetic analysis.

3 Domains
-bacterias-true bacteria,
-Archaea-procaryotes that live in extreme environments (high salt, heat, etc)
-Eukaryote-Have a nucleus and organelles.

The Origin and Evolution of Microorganisms
-Evolution states that living things change gradually through hundreds of millions of years and that these evolvements result in various types of structural and functional changes through many generations.

Systems of Presenting a Universal Tree of life
-Evolution patterns show a treelike branching from simple, primitive life forms to complex, advanced life forms.

Future Epidemics:

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In 1964 Luther Terry the surgeon general delivered a speech to Congress Saying:
"It is time to close the book on infectious disease. The war against pestilence is over."

35 years later, then Surgeon General David Satcher had different message:

"Infectious Diseases A Rising Peril; Death rates in U.S up 58% since 1980."

Reasons for this change in attitude include:

1. Microbes have changed

• Old diseases pose new threats as they become resistant to treatments MRSA, VRSA, drug-resistant tuberculosis, etc.

• There are a lot of emerging diseases from previously unknown viruses and bacteria that pose new threats example: HIV, Ebola,
  

Avian flu, SARS, etc.


2. People have changed

• Higher densities

-Earth's human population is increasing at about 200,000 people (74,000,000) annually

• More contacted with each other (increased world travel, sexual promiscuity, drug use, etc)

-75 million people per day travel by air! Thus, potentially introducing microorganisms into new areas.
Think how quickly an outbreak of a highly-infectious disease could spread

-Microorganisms are being introduced into populations of people who have never seen it before
(think of the damage done to the Native Americans when Europeans brought smallpox to the Americas).

• More encroachment into natural habitats

- Possibly coming into contact with previously unknown disease agents

• We are living longer because of advances in medicine, and as we age our immune system becomes more susceptible to infectious disease.

-How often is "pneumonia" listed as the cause of death for old people who were struggling with other health issues?
Respiratory infections, including influenza and pneumonia, are responsible for 26% of all infectious cases of death worldwide

The Metric System

Who uses the metric system?

-Everyone except:
-Liberia
-Myanmar
-United States of America

TERE- 10(12th) = 1,000,000,000,000
GIGA- 10 (9th) = 1,000,000,000
MEGA- 10 (6th) = 1,000,000
KILO- 10 (3rd) = 1,000

CENTI- 10 (-2) = 0.01
MILLI- 10 (-3) = 0.001
MICRO- 10 (-6) = 0.000001
NANO- 10 (-9) = 0.000000001



Microbial Dimensions

Bacteria generally measure in micrometers
Viruses in nanometers
Nanometer is 1/1000 of a micrometer
10x10=100 or 10^2
10x10x10=1000 or 10^3 etc…
1 mm =.001 meter (10^-3)

(side note) The earth weighs 5983 Yottagrams! It gains 40 Gg in weight yearly from cosmic dust and meteorites! (Yotta = 10 (24th) = 1,000,000,000,000,000,000,000,000)


J. Lister: English surgeon who was the first to use antiseptics in a surgical setting (1827-1912)

Semmelweis is considered the father of antiseptic procedures.

Questions

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uture Epi

1. An area of microbiology that is concerned with the occurrence of disease in human populations is?
a. immunology
b. parasitology
c. epidemiology
d. bioremediation

2. Which of the following would not be studied by a microbiologist?
a. algae
b. bacterium
c. protozoan
d. mushroom
e. none of the above

3. A cell or organism lacking a membrane-bound, structurally discrete nucleus and other sub-cellular compartments is known as a:
a. procaryote
b. eukaryote
c. protozoa
d. genome

4. A cell with a membrane-bound nucleus is known as a:
a. procaryote
b. eucaryote
c. bacteria
d. virus

5. Which of the following is not an emerging infectious disease?
a. avian influenza
b. SARS
c. common cold
d. AIDS

6. Which process involves the deliberate alteration of an organism's genetic material?
a. bioremediation
b. biotechnology
c. decomposition
d. genetic engineering

7. While out hiking you decide to save mankind by creating a new antibiotic. What will you search for on your hike?
a. Algae
b. Fungi
c. Helminths
d. All of the above

8. The Surgeon General in 1964 said" it is time to close the book on infectious disease." 53 years later the Surgeon General said " Infectious diseases a rising Peril." What are the reasons behind the change?
a. Advances in medicine
b. Human pathogens
c. Travel
d. All of the above
e. Both a & c

9. What farm grown vegetable has been genetically modified?
a. soy bean
b. corn
c. lettuce
d. tomatoes

10. Which early microbiologist was most responsible for developing sterile laboratory techniques?
a. Louis Pasteur
b. Robert Koch
c. Carl Von Linn'e
d. John Tyndall

11. How would you classify a virus?
a. procaryotic
b. eucaryotic
c. not living, unable to classify
d. fungi
e. none of the above

12. SARS was a new virus that possibly came from:
a. stray cats
b. flamingos
c. bats
d. rats
e. cockroaches

13. Who is considered the man who discovered microbiology?
a. Louis Pasteur
b. Antointe van Leeuwenhoek
c. Louis Jablot
d. Francesco Redi

14. A hypothesis can be defined as
a. a belief based on knowledge
b. knowledge based on a belief
c. a scientific explaination that is subject to testing
d. a theroy that has been thoroughly tested

The formal filing system scientists use to classify living organisims is
a. Molecular biology
b. Taxonomy
c. Scientific meathod
d. epidemiology

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