Microbiology - Chapter 1 The Main Themes of Microbiology
The Scope of Microbiology
1. Define: microorganism, microbe, microbiology
Types of Microorganisms
Know the major groups and the characteristics of each group
1. Bacteria - Archaea and Eubacteria
2. Fungi – yeasts and molds ( mycology is the study of molds)
3. Protists – slime molds, algae, diatoms & dinoflagellates, protozoa
4. Multicellular Animal Parasites – helminths: roundworms, tapeworms, flukes
Infectious Particles
1. Viruses - protein & nucleic acids
2. Prions - infectious proteins – scrapie, BSE (“mad cow disease”)
3. Viroids – infectious RNA – infect plants
Branches of Study
1. Bacteriology - the study of bacteria - new organisms from unusual environments are still being
discovered.
2. Mycology - the study of fungi (yeasts & molds) ; medical, agricultural & ecological importance; human
fungal infection rates have been rising.
3. Parasitology - the study of protozoa and helminths (parasitic worms)
4. Virology - the study of viruses - 1st virus discovered was the tobacco mosaic virus (TMV) - viruses are
not really microorganisms - not considered to be truly living - not classified in any kingdom of life
5. Immunology - the study of immunity - rapidly developing field - vaccines, immunologic tests to identify
organisms and diagnose diseases, treatment of viral diseases and cancer.
6. Public Health Microbiology and Epidemiology
7. Agricultural Microbiology
8. Biotechnology
9. Recombinant DNA technology ( = genetic engineering) - the technique by which DNA from one
organism can be inserted into another organism- bacteria are good research subjects for developing these
techniques - they are not complex cells, they reproduce rapidly & can produce large numbers of individuals
in a short time period.
Impact of Microbes on Earth
Prokaryotes – 1st cells on Earth ; 3.5 billion years ago – Fig 1.1
Eukaryotes – appeared ~ 1.8 billion years ago
Microbes are ubiquitous (everywhere)
Microbial involvement in Energy and Nutrient Flow
 Photosynthesis
 Decomposition
 Nutrient recycling
 Regulation of the Earth’s temperature ( greenhouse gases)
Underground microbes
 Weathering ; mineral extraction; soil formation
Microbial Associations with : Plants, Animals, Humans
Human Use of Microorganisms – Fig 1.3
 Biotechnology
 Genetic Engineering
 Recombinant DNA Technology
 Bioremediation
Infectious Diseases and the Human Condition – Read Insight 1.1
 Significance of human diseases – Table 1.2 ; Fig 1.4
 Normal microbial flora - beneficial organisms – normal in the body
 Pathogens – cause disease
o About 2,000 different pathogens
o 10 billion new infections worldwide each year ; 13 million deaths
 What problems in the developing world ( e.g. poverty) might contribute to the number of infections (
even from those that should be preventable)
 Emerging diseases
o Increasing or re-emerging ;– What factors are contributing to the emergence of new
infectious diseases?
 Diseases that are newly recognized as having a microbial component – Be able to give examples
 Increased antibiotic resistance in microbes
 Increased susceptibility to infectious diseases in people – Why?
General Characteristics of Microorganisms
 Prokaryotes vs. Eukaryotes – Fig 1.5 ; 1.6
 Viruses
 Microbial dimensions – see Fig 1.7 for comparisons. Not necessary to memorize exact dimensions
 Lifestyles of Microorganisms
o Free-living
o Commensals –no effect on host
o Beneficial to the host
o Parasites - live on and harm the host
History of Microbiology
Development of Microscopes - The First Observations
Robert Hooke - 1665 - first to use the term "cells" - beginning of the Cell Theory - couldn't see microbes
Anton van Leeuwenhoek - 1673-1723 - first to observe live microorganisms ( "animalcules") ( Fig 1.8 )
Modern compound microscope – mid 1800’s
The Development of Medical Microbiology
The Spontaneous Generation Debate – See Insight 1.2
1.Two opposing ideas -- spontaneous generation - theory that some forms of life could arise
spontaneously from nonliving matter. Biogenesis – the theory that all life arises from pre-existing living
forms.
2. Redi - tried to disprove the theory of spontaneous generation - experiments - rotting meat exposed to air,
but protected from flies did not grow maggots; meat that was exposed to air & flies grew maggots.
3. Rudolf Virchow -1858- Biogenesis - the theory that living cells can only arise from preexisting living
things.
4. Louis Pasteur - 1861 - resolved the issue - disproved spontaneous generation; Used S-shaped flasks boiled broth was exposed to air, but protected from microorganisms by the bent neck of the flask. Broth
remained sterile - even for long periods afterward.
The Golden Age of Microbiology 1857 - 1914
1. rapid advances in microbiology - microscopy, culture techniques, vaccines
2. Pasteur - discovered that fermentation of sugar to alcohol was caused by yeast ; spoilage of wine &
beer was caused by microorganisms. Developed method to use heat to kill most of the spoilage organisms
(called pasteurization)
3. The Germ Theory of Disease - the idea that microorganisms might cause disease.  Pasteur - a silkworm disease was caused by a protozoan parasite

Robert Koch - the first person to prove that a specific bacteria caused a specific disease linked Bacillus anthracis to anthrax in cattle.

Koch's Postulates - a sequence of experimental steps that need to be followed to prove that a
specific organism causes a specific disease.
4. Aseptic technique
 Semmelweiss - demonstrated that surgeons who didn't wash their hands were transmitting
childbirth fever, causing death in maternity wards.

Lister - introduced aseptic techniques; used carbolic acid (phenol) to disinfect surgical
wounds; proved that microorganisms could cause surgical wound infections.
Taxonomy – Three Major Areas of Taxonomy
 Nomenclature
 Classification
 Identification
Nomenclature:
1. Scientific vs. Common names – What is the advantage of using scientific names?
Common names – are rarely specific, misleading, not universal
Scientific names – specific, give meaningful information; universal
2.
Linnaeus established the system of scientific nomenclature that is used today.
 Names are usually Latin or Greek
 binomial nomenclature -- every organism is assigned two names
 the first name is the genus; the second name is the specific epithet (species
name)
 Know how to write a scientific name correctly for your lab reports and for the exam
 Names are underlined or italicized when printed.
 The genus is capitalized, the species name is written in lower case.Escherichia
coli or Staphylococcus aureus
 Genus may be abbreviated if it has already been fully spelled out in the paragraph
e.g., S. aureus
3. Used worldwide; international scientific groups are responsible for accepting and assigning names
 Standard reference for bacteria : Bergey’s Manual of Systematic Bacteriology
4. Names can change as new evidence of relationships emerges; bacteria are reclassified and
renamed. The old name is often written in parentheses.
Classification
1. classifies living organisms by establishing the relationships between them
2. used to identify an unknown organism and then group it with similar organisms
3. provides a common reference for identifying an organism that is already classified
Levels of Classification – See Fig 1.12
A. The Taxonomic Hierarchy
1. a series of subdivisions – each level or category is called a taxon.
2. What is a species? – the “biological species concept” defines a species as a group of closely
related organisms that have the ability to interbreed in nature and produce viable offspring.
Problem: How do you define a species if the organism reproduces asexually ( e.g. bacteria)?
A bacterial species is defined simply as a population of cells with similar characteristics.
3. Species that are related are grouped together into a genus.
4. Related genera make up a family.
5. Similar families are grouped into an order.
6. Similar orders make up a class.
7. Related classes make up a division ( in animals, the term phylum is used).
8. All phyla or divisions that are related are grouped into a kingdom.
9. Related kingdoms are grouped into a domain
Evolution
 Changes in organisms that occur over long periods of time
 Natural selection – the mechanism of evolution
 Adaptive, beneficial variations are preserved
 Descent with modification – all species originate from pre-existing species – all species descended
from common ancestral forms
Phylogeny – the evolutionary history or relatedness of a group of organisms; the goal of taxonomy is to
classify organisms according to their evolutionary or phylogenetic relationships.
 If two organisms shared a common evolutionary ancestor, then they should have similarities. If
they diverged from the ancestor a very long time ago, they may not have many shared
characteristics. If the split occurred very recently, they will share many more similarities.
 Modern classification is based on demonstrating the shared similarities between organisms. It is
important to use characteristics that are similar because they evolved from a common ancestor.
 What kind of information is used to determine these evolutionary relationships?
 The fossil record – used extensively in higher organisms, but doesn’t work well for bacteria.
Fossils are usually formed from the mineral or “hard” parts of the body or cell. Most
microorganisms don’t have enough of this to fossilize well.
 Some living bacteria have been isolated from amber – 25-40 million years old.
 The most useful evidence for prokaryotes is sequencing of rRNA and DNA.
Systems of Presenting a Universal Tree of Life
Linnaeus – 2 Kingdom System
 Plants and Animals
 Primarily based on morphologic similarities
The Five Kingdom System – See Fig 1.13
A. Founded by Robert Whittaker - 1969
B. Prokaryotes are the ancestors of all eukaryotes
1. prokaryotes – earliest fossils ~ 3.5 billion years ago
2. eukaryotes – earliest fossils ~ 1.4 billion years ago
3. endosymbiont theory
C. Kingdom Monera – all prokaryotic organisms are included in this kingdom
D. Other 4 kingdoms – classified mainly by
1. nutritional requirements
2. presence of “9+2” flagella
3. patterns of development
4. tissue differentiation
E. Kingdom Protista
1. simple eukaryotes ; mostly unicellular but a few are multicellular
2. have flagella at some point of their life cycle
3. lack tissue organization
4. water molds, slime molds, protozoa, algae
F. Kingdom Fungi
1. eukaryotes
2. unicellular yeasts
3. multicellular molds – have thin feeding structures, hyphae
4. mushrooms
5. Nutrition: absorptive – absorb dissolved organics through the plasma membrane
G. Kingdom Plantae
1. All are multicellular
2. Nutrition: photosynthetic autotrophs
3. Some algae, all mosses, ferns, conifers and flowering plants
H. Kingdom Animalia
1. multicellular
2. nutrients: ingestive – ingest organic matter through a mouth
3. sponges, jellyfish, worms, insects, mollusks, vertebrates (animals with backbones)
Three Domain System – Fig.1-14 – proposed by Carl Woesse 1978
Based on new information revealed by using new techniques in molecular biology. Comparing DNA
and RNA sequences can reveal relationships between organisms that may not be apparent by other means.
For bacteria, comparing ribosomal RNA from different cells is very useful.
Three distinctly different cell groups: based on rRna, tRNA, membrane lipid structure, and
sensitivity to antibiotics
1. eukaryotes
2. prokaryotes: bacteria
3. prokaryotes: archaea
A. Domain Eukarya: all eukaryotes
1. Animal, Plant, Fungus, Protist Kingdoms
B. Domain Archaea: prokaryotes
1. cell walls don’t contain peptidoglycan
2. live in extreme environments
3. have unusual metabolic processes
4. Three Kingdoms
a. Methanogens – strict anaerobes; produce methane from CO2 and H2
b. Extreme halophiles – require high concentrations of salt for survival
c. Thermoacidophiles – grow in hot, acidic environments
C. Domain Bacteria: prokaryotes
1. cell walls contain peptidoglycan
2. Gram-positive bacteria, Gram-negative bacteria, Mycoplasma, Cyanobacteria, Green non-sulfur
bacteria