THE MICROBIAL WORLD

Env.E. 202
Spring 2021
Outline

• Microbes – Introduction

• Naming & Classifying Microorganisms

• Brief History of Microbiology

• Microbes – Human Welfare

• Microbes – Diseases

• Observation of Microorganisms
Microorganisms in our Lives
• Microorganisms
are organisms that
are too small to be
seen with the
unaided eye
Microorganisms in our Lives
Good
• Decompose organic waste
• Generate oxygen by photosynthesis
• Produce chemical products such as ethanol, acetone, and
vitamins
• Produce fermented foods such as vinegar, cheese, and bread
• Produce products used in manufacturing (e.g., cellulose) and
disease treatment (e.g., insulin)
Microorganisms in our Lives
Good
• Decompose organic waste
• Generate oxygen by photosynthesis
• Produce chemical products such as ethanol, acetone, and
vitamins
• Produce fermented foods such as vinegar, cheese, and bread
• Produce products used in manufacturing (e.g., cellulose) and
disease treatment (e.g., insulin)
Bad
• A few are pathogenic (disease-producing). Also GERM
refers to a rapidly growing cell that can cause disease
Microorganisms in our Lives
• The microbiome (or microbiota) is a group of microbes that
live stably on/in the human body
– Help to maintain good health
– Can prevent growth of pathogenic microbes
– May help train the immune system to discriminate threats
Microorganisms in our Lives
• The microbiome (or microbiota) is a group of microbes that
live stably on/in the human body
– Help to maintain good health
– Can prevent growth of pathogenic microbes
– May help train the immune system to discriminate threats

• An adult human is composed of 30 trillion body cells

– Harbors another 40 trillion bacterial cells
Microorganisms in our Lives
• Normal microbiota is the collection of acquired
microorganisms on or in a healthy human being
– Begin to be acquired as newborns
– May colonize the body indefinitely
– May colonize the body fleetingly (making them transient
microbiota)
Microorganisms in our Lives
• Normal microbiota is the collection of acquired
microorganisms on or in a healthy human being
– Begin to be acquired as newborns
– May colonize the body indefinitely
– May colonize the body fleetingly (making them transient
microbiota)

• Colonization can only occur at

body sites that provide nutrients
and the right environment for the
microbes to flourish

A cluster of Escherichia coli bacteria
magnified 10,000 times
 Naming & Classifying Microorganisms
• The basic taxonomic unit is the species
• Microorganisms are generally given a genus and
species name
Escherichia coli
Genus Species
 Naming & Classifying Microorganisms
• The basic taxonomic unit is the species
• Microorganisms are generally given a genus and
species name
Escherichia coli
Genus Species
Scientific name (Systematic Name)
Binomial System of Nomenclature
 Genus name + species name
 Italicized or underlined
 Genus name is capitalized and may be
abbreviated
 Species name is never abbreviated
eg: Bacillus subtilis
B. subtilis
E.coli
 Naming & Classifying Microorganisms
• Scientific names may be descriptive or honor a
scientist
• Escherichia coli
– Honors the discoverer, Theodor Escherich
– Describes the bacterium’s habitat-the large
intestine, or colon
 Naming & Classifying Microorganisms
• Scientific names may be descriptive or honor a
scientist
• Escherichia coli
– Honors the discoverer, Theodor Escherich
– Describes the bacterium’s habitat-the large
intestine, or colon
• Staphylococcus aureus
– Describes the clustered (staphylo-)
spherical (coccus) cells
– Describes the gold-colored (aureus)
colonies
Classification of Microorganisms

Three domains:
 Bacteria

 Archaea
 Eukarya
Classification of Microorganisms

Three domains:
 Bacteria

 Archaea
 Eukarya
 Protists
 Fungi
 Plants
 Animals
Classification of Microorganisms

Three domains:
 Bacteria (prokaryotes)

 Archaea (prokaryotes)
 Eukarya (eukaryotes)
 Protists
 Fungi
 Plants
 Animals
Classification of Microorganisms
 Bacteria
• Prokaryotes
– “Prenucleus”
• Single-celled
• Peptidoglycan cell walls
• Divide via binary fission
• Derive nutrition from organic or
inorganic chemicals or photosynthesis
• May “swim” by using moving
appendages called flagella
 Archaea
• Are prokaryotes
• Lack peptidoglycan cell walls
– May lack cell wall entirely
• Often live in extreme environments
• Include:
– Methanogens
– Extreme halophiles
– Extreme thermophiles
• Generally not known to cause disease in
humans
 Fungi
• Eukaryotes
– Distinct nucleus surrounding
DNA genetic material
• Chitin cell walls
• Absorb organic chemicals for energy
• Yeasts are unicellular
• Molds and mushrooms are
multicellular
– Molds consist of masses of
mycelia, which are composed of
filaments called hyphae
 Protozoa
• Eukaryotes
• Absorb or ingest organic chemicals
• May be motile via pseudopods, cilia,
or flagella
• Free-living or parasitic (derive
nutrients from a living host)
– Some are photosynthetic
• Reproduce sexually or asexually
 Algae
• Eukaryotes
• Cellulose cell walls
• Found in freshwater, saltwater, and
soil
• Use photosynthesis for energy
– Produces oxygen and
carbohydrates
• Sexual and asexual reproduction
possible
 Viruses
• Acellular
• Consist of DNA or RNA
core
• Core is surrounded by a
protein coat
– Coat may be enclosed in
a lipid envelope
• Are replicated only when
they are in a living host cell
– Inert outside living hosts
 Multicellular Animal Parasites
• Eukaryotes
• Multicellular animals
• Not strictly microorganisms
• Parasitic flatworms and
roundworms are called
helminths
– Some microscopic
stages in their life cycles
Brief History of Microbiology
The First Observations

• 1665: Robert Hooke reported that living things are

composed of little boxes, or “cells”
• In 1858, Rudolf Virchow said cells arise from
preexisting cells.
 Marked the beginning of cell theory: All living things
are composed of cells and come from preexisting
cells
The First Observations
• The first microbes were observed from 1623 to 1673 by
Anton van Leeuwenhoek
– “Animalcules” viewed through magnifying lenses
The Debate Over Spontaneous Generation

• Spontaneous generation: the hypothesis that life arises

from nonliving matter; a “vital force” is necessary for life
• Biogenesis: the hypothesis that living cells arise only from
preexisting living cells
The Theory of Biogenesis
• 1861: Louis Pasteur demonstrated that microorganisms are
present in the air

Conditions Results
Nutrient broth placed in flask, heated, Microbial growth
NOT sealed
Nutrient broth placed in flask, heated, No Microbial growth
then immediately sealed
The Theory of Biogenesis
• 1861: Louis Pasteur demonstrated that microorganisms are
present in the air
• Pasteur also used S-shapedflasks which kept microbes out but let
air in
The Theory of Biogenesis
• 1861: Louis Pasteur demonstrated that microorganisms are
present in the air
• Pasteur also used S-shapedflasks which kept microbes out but let
air in
• Microorganisms originate in air or fluids, not mystical forces
The Theory of Biogenesis
• 1861: Louis Pasteur demonstrated that microorganisms are
present in the air
• Pasteur also used S-shapedflasks which kept microbes out but let
air in
• Microorganisms originate in air or fluids, not mystical forces
• Microbial life can be destroyed by heat formed the basis of
aseptic techniques
The Golden Age of Microbiology
• 1857-1914
• Beginning with Pasteur's work, discoveries included the
relationship between microbes and disease, immunity, and
antimicrobial drugs
Fermentation and Pasteurization
• Pasteur showed that microbes are responsible for fermentation
• Fermentation is the microbial conversion of sugar to alcohol in
the absence of air
• Microbial growth is also responsible for spoilage of food and
beverages
• Bacteria that use air spoil wine by turning it to vinegar (acetic
acid)
Fermentation and Pasteurization

• Pasteur demonstrated that these

spoilage bacteria could be killed
by heat that was not hot enough
to evaporate the alcohol in wine.
This application of a high heat
for a short time is called
pasteurization.
The Germ Theory of Disease

• 1835: Agostino Bassi showed that a silkworm disease was

caused by a fungus
• 1865: Pasteur showed that another silkworm disease was
caused by a protozoan
• 1840s: Ignaz Semmelweis advocated handwashing to prevent
transmission of puerperal fever from one obstetrical patient to
another
The Germ Theory of Disease

• 1860s: Applying Pasteur’s work showing that microbes are in

the air, can spoil food, and cause animal diseases, Joseph
Lister used a chemical antiseptic (phenol) to prevent surgical
wound infections
The Germ Theory of Disease

• 1860s: Applying Pasteur’s work showing that microbes are in

the air, can spoil food, and cause animal diseases, Joseph
Lister used a chemical antiseptic (phenol) to prevent surgical
wound infections
• 1876: Robert Koch discovered that a bacterium causes
anthrax and provided the experimental steps, Koch’s
postulates, to demonstrate that a specific microbe causes a
specific disease
The Germ Theory of Disease
Koch’s postulates

 Pathogen must be present in all cases of disease

 Pathogen must be isolated and grown in lab in pure
culture
 Pathogen from pure cultures must cause disease when
inoculated into healthy, susceptible lab animal
 Same pathogen must be isolated from the diseased lab
animal
Vaccination

• 1796: Edward Jenner inoculated a person with cowpox virus,

who was then immune to smallpox
• Vaccination is derived from the Latin word vacca, meaning
cow
• The protection is called immunity
The Birth of Modern Chemotherapy
• Treatment of disease with chemicals is called chemotherapy
• Chemotherapeutic agents used to treat infectious disease can be
synthetic drugs or antibiotics
• Antibiotics are chemicals produced by bacteria and fungi that
inhibit or kill other microbes
The Birth of Modern Chemotherapy
• Treatment of disease with chemicals is called chemotherapy
• Chemotherapeutic agents used to treat infectious disease can be
synthetic drugs or antibiotics
• Antibiotics are chemicals produced by bacteria and fungi that
inhibit or kill other microbes
• Quinine from tree bark was long used to treat malaria
• Paul Ehrlich speculated about a “magic bullet” that could destroy
a pathogen without harming the host
– 1910: Ehrlich developed a synthetic arsenic drug, salvarsan,
to treat syphilis
• 1930s: Sulfonamides were synthesized
The Birth of Modern Chemotherapy
• 1928: Alexander Fleming
discovered the first
antibiotic (by accident)
• Fleming observed that
Penicillium fungus made
an antibiotic, penicillin,
that killed S. aureus
• 1940s: Penicillin was
tested clinically and
mass-produced
Modern Developments in Microbiology
• Bacteriology is the study of bacteria
• Mycology is the study of fungi
• Parasitology is the study of protozoa and parasitic worms
• Immunology is the study of immunity
– Vaccines and interferons are used to prevent and cure
viral diseases
• Virology is the study of viruses
Modern Developments in Microbiology
Modern Developments in Microbiology
Modern Developments in Microbiology
Microbes and Human Welfare
• Microbial ecology is the study of the relationship between
microorganisms and their environment
• Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus
into forms used by plants and animals
Microbes and Human Welfare
• Microbial ecology is the study of the relationship between
microorganisms and their environment
• Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus
into forms used by plants and animals
 Microorganisms and Agriculture
 Microorganisms and Food
 Microorganisms, Energy, and the Environment
 Bioremediation
 Insect pest control by microorganisms
Microorganisms and Agriculture
 Microorganisms and Food

• Negative impacts
– Food spoilage by microorganisms requires specialized preservation
of many foods

• Positive impacts
– Microbial transformations (typically fermentations) yield

 dairy products (e.g., cheeses, yogurt, buttermilk)

 other food products (e.g., sauerkraut, pickles, leavened breads,
beer)
Microorganisms, Energy, and Environment
Bioremediation
• Bacteria degrade organic matter in sewage
• Bacteria degrade or detoxify pollutants such as oil and mercury
• Sewage is 99.9% water, with a few hundredths of 1% suspended
solids
• Treatment of sewage removes undesirable components so water
can be released or reused
– Large solids are removed physically
– Microbes are used to convert left over liquid and organic materials
into by-products such as carbon dioxide
Insect Pest Control by Microorganisms
• Microbes that are pathogenic to insects are alternatives to chemical
pesticides
– Prevent insect damage to agricultural crops and disease
transmission

• Bacillus thuringiensis infections are

fatal in many insects but harmless to
animals and plants
– The bacteria produce protein
crystals toxic to insects
– The toxin gene has been inserted
into some plants to confer insect
resistance
Modern Biotechnology and Genetic
Engineering
• Biotechnology is the use of microbes for practical applications, such as
producing foods and chemicals
• Genetic engineering is a new technique for biotechnology.
Recombinant DNA technology enables bacteria and fungi to produce
a variety of proteins, vaccines, and enzymes
– Missing or defective genes in human cells can be replaced in gene
therapy
– Genetically modified bacteria are used to protect crops from insects and
from freezing
Normal Microbiota

• Microbes normally present in and on the human body are called

normal microbiota
– Normal microbiota prevent growth of pathogens

– Normal microbiota produce growth factors such as vitamins B

and K
• Resistance is the ability of the body to ward off disease
• Resistance factors include skin, stomach acid, and antimicrobial
chemicals
Biofilms
• Microbes attach to solid surfaces and grow into masses
• They will grow on rocks, pipes, teeth, and medical implants
• Biofilms can cause infections and are often resistant to antibiotics
Infectious Diseases

• When a pathogen invades a host and overcomes the

host's resistance, disease results
• Emerging infectious diseases (EIDs): new diseases
and diseases increasing in incidence
Observing Microorganisms Through
a Microscope
Observing Microorganisms Through a
Microscope
Light Microscopy
• Any kind of microscope that uses visible light to observe
specimens
• Types of light microscopy
– Compound light microscopy
– Darkfield microscopy
– Phase-contrast microscopy
– Differential interference contrast (DIC) microscopy
– Fluorescence microscopy
– Confocal microscopy
Compound Light Microscopy
• In a compound
microscope, the
image from the
objective lens is
magnified again by
the ocular lens
• Total magnification
= objective lens ×
ocular lens
Electron Microscopy
• Uses electrons instead of light
• The shorter wavelength of electrons gives greater resolution
• Used for images too small to be seen with light microscopes, such
as viruses

 Transmission electron microscopy (TEM)

– Magnifies objects 10,000 to 10,000,000x; resolution of 10 p m

 Scanning electron microscopy (SEM)

– Magnifies objects 1,000 to 500,000x; resolution of 10 n m
Preparing Smears for Staining

• Staining: coloring microorganisms with a dye that

emphasizes certain structures
• Smear: a thin film of a material containing
microorganisms spread over a slide
• Microorganisms are fixed (attached) to the slide, which
kills the microorganisms
Preparing Smears for Staining

• Stains consist of a positive and negative ion, one of

which is colored (chromophore)
• In a basic dye, the chromophore is a cation

• In an acidic dye, the chromophore is an anion

• Staining the background instead of the cell is called
negative staining
Simple Stains
• Simple stain: use of a single basic dye

• Highlights the entire microorganism to visualize cell shapes

and structures

• A mordant may
be used to hold
the stain or coat
the specimen to
enlarge it
Differential Stains: Gram Stain
• The Gram stain classifies bacteria into gram-positive and
gram-negative
• Gram-positive bacteria tend to be killed by penicillin and
detergents.
• Gram-negative bacteria are more resistant to antibiotics.

– Gram-positive bacteria have thick peptidoglycan cell walls

– Gram-negative bacteria have thin peptidoglycan cell walls and
a layer of lipopolysaccharides
Gram Staining Procedure
Differential Stains: Gram Stain
Differential Stains: Gram Stain
Differential Stains: Gram Stain
Special Stains
• Used to distinguish parts of microorganisms
– Capsule stain
– Endospore stain
– Flagella stain
Special Stains
• Capsules are a gelatinous covering that do not accept most dyes
• Suspension of India ink or nigrosin contrasts the background with
the capsule, which appears as a halo around the cell
Special Stains to Distinguish Parts of Cells
Special Stains to Distinguish Parts of Cells