Lecture 1Intro to Microbiology: History

and Taxonomy

Microbiology

• The study of organisms to small to be seen without a microscope

• Includes living microorganisms: bacteria, algae, fungi, protozoa

• AND non-cellular infectious agents: viruses, viroids, prions

Why study Microorganisms?

• Microorganisms are the foundation for all life on earth

• They effect your everyday life

• Only a minority of microorganisms are pathogenic

• Microorganisms are found almost everywhere

Microbes and Human Welfare

• Recycle chemical elements

• Decompose organic matter

• Bioremediation

• Biotechnology

• Gene therapy

• Genetic engineering

Microbes can be used to clean up oil spills such as this one in Alaska

Courtesy of the Exxon Valdez Oil Spill Trustee Council/NOAA

Microbes and Human Disease

• Everyone has microbes in and on body

• Person may or may not contract disease once they are in contact with it

Infectious Disease

• Pathogens invade susceptible host

• Emerging infectious diseases

• Ebola

• BSE, Mad cow disease

• Know other emerging infectious diseases from book for exam

Major Groups of the Microbial World1. Bacteria

2. Archeae

3. Fungi

4. Algae

5. Protozoans

6. Helminths

7. Viruses

8. Major Features9. Small size

10. Diverse appearance

11. Diverse genetics

Bacteria

Archaea

• Found in extreme environments

Fungi

Fungi

Algae

Protozoa

Helminths

Viruses

The Spectrum of Microorganisms is Diverse

- There are over 10 million species of prokaryotes

- There are over 3600 known viruses- There are about 70,000 described species of

fungi

Discovery of Microorganisms

• Robert Hooke published Micrographia (1665)

• Anton van Leeuwenhoek (1632-1723)

• He peered at a drop of lake water through a lens that he carefully ground

Hooke’s Micrographia

© Library of Congress [LC-USZ62-95187]

Cork cells

© Library of Congress [LC-USZ62-95187]

Anton van Leeuwenhoek

Courtesy of Pfizer, Inc.

Leeuwenhoek’s drawings of bacteria

Courtesy of Royal Society, London

Next Question: Where did microorganisms originate?

• Spontaneous generation: Life originates from non-life, believed from the time of Aristotle (384-322 B.C.)

• Works of Redi, Pasteur, and Tyndall refute this theory

• Prove Germ Theory of Disease

Francesco Redi (1626-1697)

• Proponents of spontaneous generation believed that worms in rotting meat came from meat itself

• Redi debunked this theory

• Experiments with meat

New Experiments Needed to Refute Spontaneous Generation

• Typical Experiment: used nutrient broth (infusion): contains nutrients needed for microorganisms to grow

• 1. boil to kill all forms of life• 2. seal vessel• If cloudy after standing: spontaneous

generation• If clear: no spontaneous generation• Different investigators: Different results

Louis Pasteur (1822-1894)

• Father of microbiology

• Demonstrated air is filled with microorganisms

• Demonstrated that sterile infusions will stay sterile in specially constructed flasks even when they were left open to the air

John Tyndall

• Explained differences in results obtained from different laboratories

• Proved Pasteur correct

• He concluded that different infusions require different boiling times to be sterilized

• Because of heat resistant microorganisms: Endospores

Endospores

• Some microorganisms exist in two forms: – 1. a cell that is readily killed by boiling– 2. one that is heat resistant

Golden Age of Microbiology

• Rapid advances by Pasteur and Robert Koch

• Discovery of agents of many diseases and role of immunity in prevention and cure of disease

• Discoveries include:– Fermentation and pasteurization– Germ theory of disease– Vaccination

Fermentation and Pasteurization

• Pasteur- why did wine sour?

• Believed at time, that converted sugars into alcohol

• Yeasts do the work of fermentation

• Bacteria cause spoilage

• Pasteurization

Germ Theory of Disease

• Pasteur: to fight silkworm disease

• Ignaz Semmelweis: Instructed hospital staff to wash hands

• Lister: treated surgical wounds with phenol solution

• John Snow: Interviewed sick and healthy Londoners during cholera epidemic

• Robert Koch

Ignaz Semmelweiss encouraged hospital staff to wash their hands

Courtesy of Pfizer, Inc.

Robert Koch (1843-1910)

• Demonstrated that anthrax caused by Bacillus anthracis– Usual means of transmission: resistant endospores

• Introduced use of pure culture techniques for handling bacteria in lab

• Cultured bacteria on agar• Discovered Mycobacterium tuberculosis –

causative agent for tuberculosis• Proved germ theory of disease

Vaccination

• Edward Jenner:

• Introduced vaccine for smallpox

• Inoculate with fluid from cowpox blisters prevented smallpox

Modern developments in Microbiology

• Bacteriology

• Mycology

• Parasitology

• Immunology

• Virology

• Recombinant DNA technology

Taxonomy

Taxonomy

• Involves three steps:– 1. Identification– 2. Classification– 3. Nomenclature

Objective is to arrange organisms into categories that reflect the similarities of the individuals within the groups

History

• Carolus Linnaeus: 1700’s: Two Kingdoms: Plants and Animals

• Ernst Haekel: 1866: Kingdom Protista

• R.H. Whittaker: 1969: Five Kingdoms

• Carl Woese: 1990: Three Domains

Taxonomic Hierarchy

• Species: basic unit– Group of related species: strain

• Genus: group of similar species

• Family: group of similar genera, ends in - aceae• Order: group of similar families, ends in - ales• Class: group of similar orders, ends in - ia• Phylum: group of similar classes• Kingdom: group of similar Phyla• Domain: group of similar Kingdoms

Domains of the Living World

• Bacteria

• Archaea

• Eucarya– Bacteria and Archaea look identical

– Also both are prokaryotes, however differ in chemical composition and are unrelated

Eucarya

• All members of living world that are not prokaryotes are in domain eukarya

• May be single celled or multi-cellular

• Always contain true membrane-bound nucleus and other internal organelles

• Far more complex than prokaryotes

Four Kingdoms within Domain Eukarya

• Animalia– Multicellular, heterotrophic

• Plantae– Multicellular, heterotrophic

• Protista: many single celled eukaryotes– Ex. Paramecium, algae, protozoa

• Fungi– Single celled: yeast– Multicellular: molds and mushrooms

Bacteria

• Single-celled prokaryotes

• Most have specific shapes: cylindrical, spherical, and spiral

• Most have rigid cell walls

• Multiply by binary fission

• Many move using appendages

Archaea

• Have same size, shape, and appearance as bacteria

• Multiply by binary fission and move primarily with flagella

• Also have cell walls, but differ from bacteria: no peptidoglycan

• Interesting Feature: able to grow in extreme environments

Identification of Microorganisms

• Microscopic examination

• Culture characteristics

• Biochemical tests

• Nucleic Acid Analysis

• Serological Tests

• Person’s symptoms also play a role

Classification of Microorganisms

• Phenotype: Physical appearance• Genotype: Genes

– Development of molecular techniques has made this possible

• Bergey’s Manual of Systematic Bacteriology– All known species described here– If properties of newly isolated organism do not

agree with any description, considered new organism

Nomenclature

• International code for Nomenclature of Bacteria• Uses two-word naming system: Binomial

Nomenclature– First name is the Genus, capital– Second name is the species, lower case– Both are italicized– Example: Escherichia coli, or E.coli– Strains; minor differences with in species:

• E. coli strain B or E.coli strain K-12

Nonliving Members of Microbial World

• In order to be considered alive, must be composed of one or more cells

• Viruses, Viroids, and prions are termed agents

• Viruses: – Piece of nucleic acid surrounded by protein

coat– Can only multiply inside human host cells– Obligate intercellular parasites

Non-living members of the bacterial world

• Viroids:– Simpler than viruses– Single short piece of RNA– No protective coat– Can only multiply inside cells

• Prions:– Appear to only be protein without nucleic acid– Possible another agent is causing the disease